rs2799652

Variant names:

• chr6-95885976-A-C
• rs2799652

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 0.657 in 151,970 control chromosomes in the GnomAD database, including 33,105 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 0.66 (33105 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 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: 0.657 AC: 99791 AN: 151852 Hom.: 33071 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.657 AC: 99871 AN: 151970 Hom.: 33105 Cov.: 31 AF XY: 0.650 AC XY: 48266 AN XY: 74262

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.655

Alfa AF: 0.657 Hom.: 5218

Bravo AF: 0.647

Asia WGS AF: 0.613 AC: 2134 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	1.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2799652; hg19: chr6-96333852;