6-1277480-T-C

Variant names:

• chr6-1277480-T-C
• rs977673

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.478 in 152,056 control chromosomes in the GnomAD database, including 18,913 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72634 AN: 151938 Hom.: 18872 Cov.: 33

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.476

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.478 AC: 72734 AN: 152056 Hom.: 18913 Cov.: 33 AF XY: 0.489 AC XY: 36372 AN XY: 74314

African (AFR) AF: 0.634 AC: 26294 AN: 41464

American (AMR) AF: 0.428 AC: 6539 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1446 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4300 AN: 5172

South Asian (SAS) AF: 0.714 AC: 3444 AN: 4822

European-Finnish (FIN) AF: 0.464 AC: 4904 AN: 10560

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24372 AN: 67970

Other (OTH) AF: 0.482 AC: 1016 AN: 2106

Alfa AF: 0.419 Hom.: 2469

Bravo AF: 0.475

Asia WGS AF: 0.797 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs977673; hg19: chr6-1277715; COSMIC: COSV52859166;