rs2799644

Variant names:

• chr6-95910286-A-G
• rs2799644

Your query was ambiguous. Multiple possible variants found:

• chr6-95910286-A-G
• chr6-95910286-A-T

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 0.587 in 151,946 control chromosomes in the GnomAD database, including 26,803 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 0.59 (26803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 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: 0.587 AC: 89059 AN: 151828 Hom.: 26774 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.587 AC: 89133 AN: 151946 Hom.: 26803 Cov.: 31 AF XY: 0.583 AC XY: 43296 AN XY: 74250

African (AFR) AF: 0.481 AC: 19934 AN: 41456

American (AMR) AF: 0.502 AC: 7654 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2238 AN: 5162

South Asian (SAS) AF: 0.615 AC: 2957 AN: 4810

European-Finnish (FIN) AF: 0.664 AC: 7012 AN: 10554

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45083 AN: 67922

Other (OTH) AF: 0.601 AC: 1271 AN: 2114

Alfa AF: 0.642 Hom.: 24495

Bravo AF: 0.568

Asia WGS AF: 0.555 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.80
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs2799644; hg19: chr6-96358162;