rs4760516

Variant names:

• chr12-92990459-G-A
• rs4760516

Your query was ambiguous. Multiple possible variants found:

• chr12-92990459-G-A
• chr12-92990459-G-C
• chr12-92990459-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 0.634 in 151,888 control chromosomes in the GnomAD database, including 30,939 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 0.63 (30939 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.634 AC: 96279 AN: 151770 Hom.: 30928 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.634 AC: 96317 AN: 151888 Hom.: 30939 Cov.: 31 AF XY: 0.637 AC XY: 47268 AN XY: 74198

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.622

Alfa AF: 0.656 Hom.: 42988

Bravo AF: 0.630

Asia WGS AF: 0.676 AC: 2348 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
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: rs4760516; hg19: chr12-93384235;