rs4476964

Variant names:

• chr8-31635152-C-T
• rs4476964

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 0.231 in 152,032 control chromosomes in the GnomAD database, including 4,084 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 0.23 (4084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.231 AC: 35037 AN: 151914 Hom.: 4078 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.231 AC: 35052 AN: 152032 Hom.: 4084 Cov.: 32 AF XY: 0.231 AC XY: 17143 AN XY: 74286

African (AFR) AF: 0.216 AC: 8938 AN: 41456

American (AMR) AF: 0.253 AC: 3870 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1624 AN: 5160

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4824

European-Finnish (FIN) AF: 0.215 AC: 2265 AN: 10550

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15725 AN: 67988

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.226 Hom.: 850

Bravo AF: 0.232

Asia WGS AF: 0.282 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.78
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs4476964; hg19: chr8-31492668;