rs4761097

Positions:

• chr12-84793732-G-A
• chr12-84793732-G-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 0.564 in 151,880 control chromosomes in the GnomAD database, including 24,523 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 (24523 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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: 0.564 AC: 85641 AN: 151762 Hom.: 24497 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.564 AC: 85706 AN: 151880 Hom.: 24523 Cov.: 32 AF XY: 0.564 AC XY: 41837 AN XY: 74208

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.584

Alfa AF: 0.553 Hom.: 12505

Bravo AF: 0.581

Asia WGS AF: 0.618 AC: 2146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4761097; hg19: chr12-85187511;