dbSNP rs55909016: GOLGA6L7:p.Lys301Glu (chr15-28843203-T-C) – 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_001365371.2(GOLGA6L7):c.901A>G(p.Lys301Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000549 in 429,756 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 3 hom., cov: 34)

Exomes 𝑓: 0.00017 ( 1 hom. )

Consequence

GOLGA6L7
NM_001365371.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.04

Publications

0 publications found

Variant links:

Genes affected

GOLGA6L7 (HGNC:37442): (golgin A6 family like 7) Predicted to be located in cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA6L7 links:

ENSG00000290880 (HGNC:):

ENSG00000290880 links:

PDCD6IPP2 (HGNC:49873): (PDCD6IP pseudogene 2)

PDCD6IPP2 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=0.02998504).

BP6

Variant 15-28843203-T-C is Benign according to our data. Variant chr15-28843203-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3770832.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365371.2. 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
	GOLGA6L7	NM_001365371.2	MANE Select	c.901A>G	p.Lys301Glu	missense	Exon 9 of 9	NP_001352300.1	A0A1B0GV03
	PDCD6IPP2	NR_037599.1		n.1561-3536T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GOLGA6L7	ENST00000567390.7	TSL:5 MANE Select	c.901A>G	p.Lys301Glu	missense	Exon 9 of 9	ENSP00000490318.1	A0A1B0GV03
ENSG00000290880	ENST00000564604.5	TSL:4	n.369-3536T>C		intron	N/A
ENSG00000290880	ENST00000566178.7	TSL:5	n.506-3536T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00154

AC:

184

AN:

119818

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00530

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000576

Gnomad FIN

AF:

0.000115

Gnomad MID

AF:

0.00481

Gnomad NFE

AF:

0.000205

Gnomad OTH

AF:

0.00303

GnomAD4 exome

AF:

0.000168

AC:

AN:

309858

Hom.:

Cov.:

AF XY:

0.000145

AC XY:

AN XY:

159128

show subpopulations

African (AFR)

AF:

0.00432

AC:

AN:

6710

American (AMR)

AF:

0.000236

AC:

AN:

8484

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9610

East Asian (EAS)

AF:

0.0000442

AC:

AN:

22636

South Asian (SAS)

AF:

0.0000722

AC:

AN:

13856

European-Finnish (FIN)

AF:

0.00

AC:

AN:

23508

Middle Eastern (MID)

AF:

0.000720

AC:

AN:

1388

European-Non Finnish (NFE)

AF:

0.0000536

AC:

AN:

205050

Other (OTH)

AF:

0.000376

AC:

AN:

18616

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.456

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.00153

AC:

184

AN:

119898

Hom.:

Cov.:

AF XY:

0.00152

AC XY:

AN XY:

58566

show subpopulations

African (AFR)

AF:

0.00529

AC:

147

AN:

27794

American (AMR)

AF:

0.00131

AC:

AN:

12220

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2962

East Asian (EAS)

AF:

0.00

AC:

AN:

3644

South Asian (SAS)

AF:

0.000576

AC:

AN:

3470

European-Finnish (FIN)

AF:

0.000115

AC:

AN:

8724

Middle Eastern (MID)

AF:

0.00505

AC:

AN:

198

European-Non Finnish (NFE)

AF:

0.000205

AC:

AN:

58476

Other (OTH)

AF:

0.00300

AC:

AN:

1664

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

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:

0.0239

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_noAF

Benign

-0.84

CADD

Benign

0.57

(source)

DANN

Benign

0.22

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.62

MetaRNN

Benign

0.030

PhyloP100

-1.0

GERP RS

0.43

Varity_R

0.050

gMVP

0.0045

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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