rs12676327

Positions:

• chr8-29639246-T-G

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 0.556 in 151,984 control chromosomes in the GnomAD database, including 25,592 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 0.56 (25592 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.728 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: 0.556 AC: 84511 AN: 151864 Hom.: 25595 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.556 AC: 84537 AN: 151984 Hom.: 25592 Cov.: 31 AF XY: 0.562 AC XY: 41760 AN XY: 74312

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.573

Alfa AF: 0.622 Hom.: 16310

Bravo AF: 0.539

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12676327; hg19: chr8-29496762;