rs1472750

Positions:

• chr10-113475355-T-C

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 0.918 in 152,216 control chromosomes in the GnomAD database, including 64,209 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 0.92 (64209 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139696 AN: 152098 Hom.: 64171 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.918 AC: 139786 AN: 152216 Hom.: 64209 Cov.: 31 AF XY: 0.918 AC XY: 68313 AN XY: 74400

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.948

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.922

Alfa AF: 0.909 Hom.: 29238

Bravo AF: 0.922

Asia WGS AF: 0.944 AC: 3284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472750; hg19: chr10-115235114;