rs4760506

Variant names:

• chr12-92939274-A-G
• rs4760506

Your query was ambiguous. Multiple possible variants found:

• chr12-92939274-A-G
• chr12-92939274-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.545 in 152,008 control chromosomes in the GnomAD database, including 22,802 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 0.55 (22802 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.631 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: 0.546 AC: 82875 AN: 151890 Hom.: 22785 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.545 AC: 82913 AN: 152008 Hom.: 22802 Cov.: 32 AF XY: 0.545 AC XY: 40493 AN XY: 74322

African (AFR) AF: 0.534 AC: 22135 AN: 41442

American (AMR) AF: 0.620 AC: 9472 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1904 AN: 3464

East Asian (EAS) AF: 0.650 AC: 3350 AN: 5156

South Asian (SAS) AF: 0.488 AC: 2352 AN: 4818

European-Finnish (FIN) AF: 0.522 AC: 5518 AN: 10580

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36435 AN: 67972

Other (OTH) AF: 0.541 AC: 1139 AN: 2106

Alfa AF: 0.542 Hom.: 71700

Bravo AF: 0.558

Asia WGS AF: 0.538 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.99
DANN	Benign	0.76
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs4760506; hg19: chr12-93333050;