rs4646249

Variant names:

• chr8-18402921-T-G
• rs4646249

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 0.689 in 151,968 control chromosomes in the GnomAD database, including 36,849 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 0.69 (36849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.690 AC: 104733 AN: 151850 Hom.: 36839 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.689 AC: 104781 AN: 151968 Hom.: 36849 Cov.: 31 AF XY: 0.683 AC XY: 50712 AN XY: 74276

African (AFR) AF: 0.735 AC: 30465 AN: 41460

American (AMR) AF: 0.573 AC: 8741 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2779 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1506 AN: 5142

South Asian (SAS) AF: 0.696 AC: 3335 AN: 4792

European-Finnish (FIN) AF: 0.680 AC: 7183 AN: 10566

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48488 AN: 67958

Other (OTH) AF: 0.687 AC: 1450 AN: 2110

Alfa AF: 0.710 Hom.: 63087

Bravo AF: 0.677

Asia WGS AF: 0.520 AC: 1811 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	1.3
DANN	Benign	0.55
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4646249; hg19: chr8-18260431;