chr6-95885976-A-C

Variant names:

• chr6-95885976-A-C
• rs2799652

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 0.657 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.662 AC: 27422 AN: 41438

American (AMR) AF: 0.544 AC: 8304 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2292 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2460 AN: 5162

South Asian (SAS) AF: 0.694 AC: 3339 AN: 4810

European-Finnish (FIN) AF: 0.656 AC: 6923 AN: 10550

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46968 AN: 67964

Other (OTH) AF: 0.655 AC: 1382 AN: 2110

Alfa AF: 0.656 Hom.: 5384

Bravo AF: 0.647

Asia WGS AF: 0.613 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2799652; hg19: chr6-96333852;