rs2799644

Positions:

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

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 0.587 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.601

Alfa AF: 0.643 Hom.: 18337

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2799644; hg19: chr6-96358162;