6-49403271-T-C

Variant names:

• chr6-49403271-T-C
• rs2501976

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 0.645 in 151,774 control chromosomes in the GnomAD database, including 31,754 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 0.65 (31754 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 13 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 = 0.76 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: 0.645 AC: 97834 AN: 151654 Hom.: 31727 Cov.: 30

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.645 AC: 97910 AN: 151774 Hom.: 31754 Cov.: 30 AF XY: 0.648 AC XY: 48072 AN XY: 74148

African (AFR) AF: 0.621 AC: 25741 AN: 41418

American (AMR) AF: 0.745 AC: 11309 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2166 AN: 3466

East Asian (EAS) AF: 0.780 AC: 4022 AN: 5154

South Asian (SAS) AF: 0.635 AC: 3052 AN: 4804

European-Finnish (FIN) AF: 0.630 AC: 6648 AN: 10556

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42731 AN: 67880

Other (OTH) AF: 0.667 AC: 1405 AN: 2106

Alfa AF: 0.642 Hom.: 17504

Bravo AF: 0.657

Asia WGS AF: 0.658 AC: 2288 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	3.2
DANN	Benign	0.51
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2501976; hg19: chr6-49370984;