15-20534587-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1

The NM_001145004.2(GOLGA6L6):​c.1847C>T​(p.Thr616Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 97,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0039 ( 8 hom. )
Failed GnomAD Quality Control

Consequence

GOLGA6L6
NM_001145004.2 missense

Scores

1
13

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.18
Variant links:
Genes affected
GOLGA6L6 (HGNC:37225): (golgin A6 family like 6)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

PM2
Variant has high frequency in the AFR(0.00867279) population. However there is too low homozygotes in high coverage region: (expected more than 22, got 0).
BP4
Computational evidence support a benign effect (MetaRNN=0.0030660033).
BP6
Variant 15-20534587-G-A is Benign according to our data. Variant chr15-20534587-G-A is described in ClinVar as [Benign]. Clinvar id is 402906.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0302 (2941/97252) while in subpopulation AFR AF= 0.0425 (995/23426). AF 95% confidence interval is 0.0403. There are 0 homozygotes in gnomad4. There are 1382 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GOLGA6L6NM_001145004.2 linkc.1847C>T p.Thr616Met missense_variant Exon 8 of 9 ENST00000619213.1 NP_001138476.2 A8MZA4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOLGA6L6ENST00000619213.1 linkc.1847C>T p.Thr616Met missense_variant Exon 8 of 9 5 NM_001145004.2 ENSP00000480376.1 A8MZA4

Frequencies

GnomAD3 genomes
AF:
0.0303
AC:
2945
AN:
97150
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0427
Gnomad AMI
AF:
0.0115
Gnomad AMR
AF:
0.0200
Gnomad ASJ
AF:
0.0177
Gnomad EAS
AF:
0.00129
Gnomad SAS
AF:
0.0176
Gnomad FIN
AF:
0.0295
Gnomad MID
AF:
0.0362
Gnomad NFE
AF:
0.0307
Gnomad OTH
AF:
0.0302
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00387
AC:
4674
AN:
1208304
Hom.:
8
Cov.:
66
AF XY:
0.00376
AC XY:
2242
AN XY:
595844
show subpopulations
Gnomad4 AFR exome
AF:
0.00965
Gnomad4 AMR exome
AF:
0.00350
Gnomad4 ASJ exome
AF:
0.00273
Gnomad4 EAS exome
AF:
0.0000883
Gnomad4 SAS exome
AF:
0.00125
Gnomad4 FIN exome
AF:
0.00605
Gnomad4 NFE exome
AF:
0.00396
Gnomad4 OTH exome
AF:
0.00430
GnomAD4 genome
AF:
0.0302
AC:
2941
AN:
97252
Hom.:
0
Cov.:
34
AF XY:
0.0290
AC XY:
1382
AN XY:
47672
show subpopulations
Gnomad4 AFR
AF:
0.0425
Gnomad4 AMR
AF:
0.0199
Gnomad4 ASJ
AF:
0.0177
Gnomad4 EAS
AF:
0.00130
Gnomad4 SAS
AF:
0.0179
Gnomad4 FIN
AF:
0.0295
Gnomad4 NFE
AF:
0.0306
Gnomad4 OTH
AF:
0.0299
Alfa
AF:
0.0570
Hom.:
18
ExAC
AF:
0.0675
AC:
1379

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 28, 2016Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.057
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.74
CADD
Benign
0.24
DANN
Benign
0.22
DEOGEN2
Benign
0.00060
T
Eigen
Benign
-0.89
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.00091
N
LIST_S2
Benign
0.23
T
MetaRNN
Benign
0.0031
T
MetaSVM
Benign
-1.0
T
PrimateAI
Uncertain
0.56
T
Sift4G
Benign
0.22
T
Vest4
0.035
ClinPred
0.016
T
Varity_R
0.015
gMVP
0.0038

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs28590435; hg19: chr15-20739825; COSMIC: COSV71180651; API