dbSNP rs562628195: GOLGA6L22:p.Glu664Gly (chr15-22466251-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001396956.1(GOLGA6L22):c.1991A>G(p.Glu664Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.010 ( 28 hom., cov: 12)

Exomes 𝑓: 0.010 ( 829 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L22
NM_001396956.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0940

Publications

1 publications found

Variant links:

Genes affected

GOLGA6L22 (HGNC:50289): (golgin A6 family like 22)

GOLGA6L22 links:

ENSG00000310081 (HGNC:):

ENSG00000310081 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0063911676).

BP6

Variant 15-22466251-A-G is Benign according to our data. Variant chr15-22466251-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2644963.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 28 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396956.1. 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
	GOLGA6L22	NM_001396956.1	MANE Select	c.1991A>G	p.Glu664Gly	missense	Exon 8 of 9	NP_001383885.1	H0YM25
	GOLGA6L22	NM_001396957.1		c.1988A>G	p.Glu663Gly	missense	Exon 8 of 9	NP_001383886.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L22	ENST00000622895.2	TSL:5 MANE Select	c.1991A>G	p.Glu664Gly	missense	Exon 8 of 9	ENSP00000483673.2	H0YM25
	ENSG00000310081	ENST00000846990.1		n.151+4160T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0105

AC:

851

AN:

81224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00187

Gnomad AMI

AF:

0.0431

Gnomad AMR

AF:

0.00680

Gnomad ASJ

AF:

0.000972

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00395

Gnomad FIN

AF:

0.0237

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0144

Gnomad OTH

AF:

0.00690

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00997

AC:

8258

AN:

828432

Hom.:

829

Cov.:

AF XY:

0.00977

AC XY:

4164

AN XY:

426194

show subpopulations

African (AFR)

AF:

0.00221

AC:

AN:

19490

American (AMR)

AF:

0.00576

AC:

183

AN:

31756

Ashkenazi Jewish (ASJ)

AF:

0.00145

AC:

AN:

19252

East Asian (EAS)

AF:

0.00

AC:

AN:

32406

South Asian (SAS)

AF:

0.00195

AC:

125

AN:

64086

European-Finnish (FIN)

AF:

0.0375

AC:

1273

AN:

33942

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2522

European-Non Finnish (NFE)

AF:

0.0105

AC:

6164

AN:

587032

Other (OTH)

AF:

0.0116

AC:

442

AN:

37946

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

317

634

952

1269

1586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.0105

AC:

850

AN:

81280

Hom.:

Cov.:

AF XY:

0.0107

AC XY:

419

AN XY:

39110

show subpopulations

African (AFR)

AF:

0.00192

AC:

AN:

18254

American (AMR)

AF:

0.00679

AC:

AN:

7658

Ashkenazi Jewish (ASJ)

AF:

0.000972

AC:

AN:

2058

East Asian (EAS)

AF:

0.00

AC:

AN:

2776

South Asian (SAS)

AF:

0.00282

AC:

AN:

1772

European-Finnish (FIN)

AF:

0.0237

AC:

127

AN:

5356

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0144

AC:

604

AN:

41884

Other (OTH)

AF:

0.00681

AC:

AN:

1028

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

123

154

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.0119

Hom.:

ClinVar

ClinVar submissions

Significance:Likely 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

Benign

0.12

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.88

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.95

FATHMM_MKL

Benign

0.0087

LIST_S2

Benign

0.36

M_CAP

Benign

0.0015

MetaRNN

Benign

0.0064

MetaSVM

Benign

-1.0

PhyloP100

-0.094

PrimateAI

Uncertain

0.53

Sift4G

Benign

0.24

Vest4

0.083

MVP

0.092

ClinPred

0.15

Varity_R

0.038

gMVP

0.0057

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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