rs4761130

Variant names:

• chr12-85308487-C-T
• rs4761130

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 0.497 in 151,816 control chromosomes in the GnomAD database, including 22,425 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 0.50 (22425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 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: 0.497 AC: 75448 AN: 151698 Hom.: 22406 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.497 AC: 75474 AN: 151816 Hom.: 22425 Cov.: 32 AF XY: 0.499 AC XY: 37027 AN XY: 74192

African (AFR) AF: 0.155 AC: 6432 AN: 41440

American (AMR) AF: 0.591 AC: 9009 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2217 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2373 AN: 5158

South Asian (SAS) AF: 0.674 AC: 3251 AN: 4822

European-Finnish (FIN) AF: 0.578 AC: 6102 AN: 10552

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44160 AN: 67832

Other (OTH) AF: 0.565 AC: 1190 AN: 2106

Alfa AF: 0.563 Hom.: 3307

Bravo AF: 0.479

Asia WGS AF: 0.553 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.078
DANN	Benign	0.48
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4761130; hg19: chr12-85702265;