rs17200983

Variant names:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001003693.3(LY6G6F):c.101C>A(p.Pro34Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00353 in 1,614,166 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0091 ( 18 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 83 hom. )

Consequence

LY6G6F
NM_001003693.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.60

Publications

9 publications found

Variant links:

Genes affected

LY6G6F (HGNC:13933): (lymphocyte antigen 6 family member G6F) The human G6f protein is a type I transmembrane protein belonging to the immunoglobin (Ig) superfamily, which is comprised of cell-surface proteins involved in the immune system and cellular recognition (de Vet et al., 2003 [PubMed 12852788]).[supplied by OMIM, Mar 2008]

LY6G6F links:

LY6G6F-LY6G6D (HGNC:38821): (LY6G6F-LY6G6D readthrough) This locus represents naturally occurring readthrough transcription between the neighboring LY6G6F (lymphocyte antigen 6 family member G6F) and LY6G6D (lymphocyte antigen 6 family member G6D) genes on chromosome 6. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jul 2017]

LY6G6F-LY6G6D links:

ENSG00000204422 (HGNC:):

ENSG00000204422 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010085255).

BP6

Variant 6-31707506-C-A is Benign according to our data. Variant chr6-31707506-C-A is described in ClinVar as Benign. ClinVar VariationId is 780983.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00905 (1379/152306) while in subpopulation AFR AF = 0.0272 (1129/41548). AF 95% confidence interval is 0.0259. There are 18 homozygotes in GnomAd4. There are 664 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 18 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001003693.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY6G6F	NM_001003693.3	MANE Select	c.101C>A	p.Pro34Gln	missense	Exon 2 of 6	NP_001003693.1	Q5SQ64-1
	LY6G6F-LY6G6D	NM_001353334.2		c.101C>A	p.Pro34Gln	missense	Exon 2 of 6	NP_001340263.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
LY6G6F	ENST00000375832.5	TSL:1 MANE Select	c.101C>A	p.Pro34Gln	missense	Exon 2 of 6	ENSP00000364992.5	Q5SQ64-1
LY6G6F-LY6G6D	ENST00000503322.1	TSL:1	c.101C>A	p.Pro34Gln	missense	Exon 2 of 6	ENSP00000421232.1
ENSG00000204422	ENST00000461287.1	TSL:2	n.537+4511G>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00904

AC:

1376

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0272

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.0129

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00109

Gnomad OTH

AF:

0.0105

GnomAD2 exomes

AF:

0.00439

AC:

1103

AN:

251222

AF XY:

0.00360

show subpopulations

Gnomad AFR exome

AF:

0.0318

Gnomad AMR exome

AF:

0.00448

Gnomad ASJ exome

AF:

0.00179

Gnomad EAS exome

AF:

0.0110

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.00125

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00296

AC:

4320

AN:

1461860

Hom.:

Cov.:

AF XY:

0.00282

AC XY:

2053

AN XY:

727224

show subpopulations

African (AFR)

AF:

0.0314

AC:

1050

AN:

33480

American (AMR)

AF:

0.00420

AC:

188

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00222

AC:

AN:

26134

East Asian (EAS)

AF:

0.0434

AC:

1722

AN:

39698

South Asian (SAS)

AF:

0.00183

AC:

158

AN:

86250

European-Finnish (FIN)

AF:

0.0000749

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.00954

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.000807

AC:

897

AN:

1111996

Other (OTH)

AF:

0.00311

AC:

188

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

286

572

859

1145

1431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

148

222

296

370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00905

AC:

1379

AN:

152306

Hom.:

Cov.:

AF XY:

0.00892

AC XY:

664

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.0272

AC:

1129

AN:

41548

American (AMR)

AF:

0.00418

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00346

AC:

AN:

3470

East Asian (EAS)

AF:

0.0129

AC:

AN:

5192

South Asian (SAS)

AF:

0.00145

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0000941

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00109

AC:

AN:

68030

Other (OTH)

AF:

0.0104

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

127

190

254

317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00437

Hom.:

Bravo

AF:

0.0101

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.0325

AC:

143

ESP6500EA

AF:

0.000581

AC:

ExAC

AF:

0.00501

AC:

608

Asia WGS

AF:

0.0110

AC:

AN:

3478

EpiCase

AF:

0.00174

EpiControl

AF:

0.00207

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.34

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.31

CADD

Uncertain

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.042

Eigen

Uncertain

0.56

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.61

MetaRNN

Benign

0.010

MetaSVM

Benign

-0.60

MutationAssessor

Uncertain

2.2

PhyloP100

3.6

PrimateAI

Benign

0.42

PROVEAN

Pathogenic

-5.2

REVEL

Benign

0.14

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.0090

Polyphen

0.99

Vest4

0.53

MVP

0.80

MPC

0.41

ClinPred

0.033

GERP RS

4.8

Varity_R

0.14

gMVP

0.39

Mutation Taster

=95/5

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over