rs644377

Variant names:

• chr6-152897549-A-T
• rs644377

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 0.539 in 151,968 control chromosomes in the GnomAD database, including 22,621 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 0.54 (22621 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.641 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: 0.539 AC: 81830 AN: 151850 Hom.: 22585 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.539 AC: 81920 AN: 151968 Hom.: 22621 Cov.: 32 AF XY: 0.542 AC XY: 40244 AN XY: 74278

African (AFR) AF: 0.637 AC: 26384 AN: 41440

American (AMR) AF: 0.619 AC: 9461 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2596 AN: 5142

South Asian (SAS) AF: 0.660 AC: 3181 AN: 4822

European-Finnish (FIN) AF: 0.462 AC: 4867 AN: 10546

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32239 AN: 67958

Other (OTH) AF: 0.517 AC: 1092 AN: 2114

Alfa AF: 0.497 Hom.: 2352

Bravo AF: 0.552

Asia WGS AF: 0.605 AC: 2101 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.95
DANN	Benign	0.49
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs644377; hg19: chr6-153218684; COSMIC: COSV69403967;