15-20534419-A-G

Variant names:

• chr15-20534419-A-G
• rs4932675
• NM_001145004.2:c.2015T>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001145004.2(GOLGA6L6):​c.2015T>C​(p.Met672Thr) 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 0.0012 (0 hom., cov: 21)
  • Exomes 𝑓: 0.00011 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L6 NM_001145004.2 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -1.64

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.104261935).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L6	NM_001145004.2	c.2015T>C	p.Met672Thr	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.2015T>C	p.Met672Thr	missense_variant	Exon 8 of 9	5	NM_001145004.2	ENSP00000480376.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 140 AN: 115764 Hom.: 0 Cov.: 21 FAILED QC

Gnomad AFR AF: 0.00162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00161

Gnomad ASJ AF: 0.00103

Gnomad EAS AF: 0.000724

Gnomad SAS AF: 0.00123

Gnomad FIN AF: 0.00108

Gnomad MID AF: 0.00549

Gnomad NFE AF: 0.00102

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000110 AC: 136 AN: 1238484 Hom.: 0 Cov.: 31 AF XY: 0.000114 AC XY: 70 AN XY: 614698

Gnomad4 AFR exome AF: 0.000152

Gnomad4 AMR exome AF: 0.000260

Gnomad4 ASJ exome AF: 0.0000873

Gnomad4 EAS exome AF: 0.0000301

Gnomad4 SAS exome AF: 0.000155

Gnomad4 FIN exome AF: 0.000176

Gnomad4 NFE exome AF: 0.0000990

Gnomad4 OTH exome AF: 0.000155

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00121 AC: 140 AN: 115836 Hom.: 0 Cov.: 21 AF XY: 0.00123 AC XY: 69 AN XY: 55984

Gnomad4 AFR AF: 0.00162

Gnomad4 AMR AF: 0.00161

Gnomad4 ASJ AF: 0.00103

Gnomad4 EAS AF: 0.000726

Gnomad4 SAS AF: 0.00154

Gnomad4 FIN AF: 0.00108

Gnomad4 NFE AF: 0.00102

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000833 Hom.: 0

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	0.26
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	1.5
DANN	Benign	0.23
DEOGEN2	Benign	0.038	T
Eigen	Benign	-0.95
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.010	N
LIST_S2	Benign	0.30	T
M_CAP	Benign	0.0036	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-0.97	T
PrimateAI	Uncertain	0.61	T
Sift4G	Benign	0.45	T
Vest4		0.094
MVP		0.040
ClinPred		0.11	T
Varity_R		0.038
gMVP		0.019

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: rs4932675; hg19: chr15-20739657; COSMIC: COSV71181440;