rs4452759

Positions:

• chr8-31629934-C-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 0.406 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

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.399

Alfa AF: 0.460 Hom.: 33089

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4452759; hg19: chr8-31487450;