chr8-31629934-C-T

Variant names:

• chr8-31629934-C-T
• rs4452759

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 0.406 in 151,964 control chromosomes in the GnomAD database, including 13,200 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 0.41 (13200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.505 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: 0.407 AC: 61757 AN: 151846 Hom.: 13193 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.406 AC: 61773 AN: 151964 Hom.: 13200 Cov.: 32 AF XY: 0.407 AC XY: 30222 AN XY: 74272

African (AFR) AF: 0.268 AC: 11127 AN: 41460

American (AMR) AF: 0.515 AC: 7858 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2152 AN: 5162

South Asian (SAS) AF: 0.390 AC: 1877 AN: 4814

European-Finnish (FIN) AF: 0.400 AC: 4220 AN: 10542

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31844 AN: 67940

Other (OTH) AF: 0.399 AC: 840 AN: 2106

Alfa AF: 0.451 Hom.: 49200

Bravo AF: 0.410

Asia WGS AF: 0.431 AC: 1500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4452759; hg19: chr8-31487450;