15-20534396-A-C

Variant names:

• chr15-20534396-A-C
• rs4932676
• NM_001145004.2:c.2038T>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001145004.2(GOLGA6L6):​c.2038T>G​(p.Trp680Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.11 (0 hom., cov: 7)
  • Exomes 𝑓: 0.023 (10 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L6 NM_001145004.2 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -5.44

Genes affected

GOLGA6L6 (HGNC:37225): (golgin A6 family like 6)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.006571591).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L6	NM_001145004.2	c.2038T>G	p.Trp680Gly	missense_variant	Exon 8 of 9	ENST00000619213.1	NP_001138476.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L6	ENST00000619213.1	c.2038T>G	p.Trp680Gly	missense_variant	Exon 8 of 9	5	NM_001145004.2	ENSP00000480376.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 5484 AN: 50982 Hom.: 0 Cov.: 7

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0909

GnomAD3 exomes AF: 0.00383 AC: 429 AN: 111990 Hom.: 0 AF XY: 0.00343 AC XY: 210 AN XY: 61186

Gnomad AFR exome AF: 0.00777

Gnomad AMR exome AF: 0.00499

Gnomad ASJ exome AF: 0.000929

Gnomad EAS exome AF: 0.00575

Gnomad SAS exome AF: 0.00280

Gnomad FIN exome AF: 0.000165

Gnomad NFE exome AF: 0.00404

Gnomad OTH exome AF: 0.00387

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0233 AC: 18019 AN: 774024 Hom.: 10 Cov.: 27 AF XY: 0.0225 AC XY: 8748 AN XY: 389626

Gnomad4 AFR exome AF: 0.0331

Gnomad4 AMR exome AF: 0.0156

Gnomad4 ASJ exome AF: 0.0114

Gnomad4 EAS exome AF: 0.00438

Gnomad4 SAS exome AF: 0.0238

Gnomad4 FIN exome AF: 0.00675

Gnomad4 NFE exome AF: 0.0255

Gnomad4 OTH exome AF: 0.0221

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.108 AC: 5487 AN: 51038 Hom.: 0 Cov.: 7 AF XY: 0.102 AC XY: 2534 AN XY: 24848

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0992

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0374

Gnomad4 SAS AF: 0.0963

Gnomad4 FIN AF: 0.0812

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.00835 Hom.: 1

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

-

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.029
DANN	Benign	0.29
DEOGEN2	Benign	0.0025	T
Eigen	Benign	-2.3
Eigen_PC	Benign	-2.4
FATHMM_MKL	Benign	0.00042	N
LIST_S2	Benign	0.056	T
M_CAP	Benign	0.0033	T
MetaRNN	Benign	0.0066	T
MetaSVM	Benign	-1.0	T
PrimateAI	Uncertain	0.53	T
Sift4G	Benign	0.69	T
Vest4		0.099
MVP		0.030
ClinPred		0.0020	T
Varity_R		0.065
gMVP		0.0035

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

Other links and lift over

dbSNP: rs4932676; hg19: chr15-20739634; COSMIC: COSV71181479;