rs4751264

Variant names:

• chr10-130740310-G-A
• rs4751264

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 0.091 in 152,048 control chromosomes in the GnomAD database, including 827 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 0.091 (827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 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: 0.0910 AC: 13825 AN: 151930 Hom.: 825 Cov.: 32

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0892

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0910 AC: 13840 AN: 152048 Hom.: 827 Cov.: 32 AF XY: 0.0908 AC XY: 6744 AN XY: 74298

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0868

Gnomad4 EAS AF: 0.0964

Gnomad4 SAS AF: 0.0872

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.111 Hom.: 698

Bravo AF: 0.0891

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4751264; hg19: chr10-132538574;