6-1277480-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.482

Alfa AF: 0.413 Hom.: 2329

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

Splicing

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

Publications

LitVar

Other links and lift over

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