chr8-31638152-A-T

Position:

• chr8-31638152-A-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 0.7 in 152,018 control chromosomes in the GnomAD database, including 37,732 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 0.70 (37732 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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: 0.700 AC: 106402 AN: 151900 Hom.: 37712 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.700 AC: 106457 AN: 152018 Hom.: 37732 Cov.: 31 AF XY: 0.701 AC XY: 52136 AN XY: 74324

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.717

Alfa AF: 0.724 Hom.: 4993

Bravo AF: 0.693

Asia WGS AF: 0.661 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7014762; hg19: chr8-31495668;