rs751160

Variant names:

• chr10-98310283-G-C
• rs751160

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 0.26 in 151,926 control chromosomes in the GnomAD database, including 5,967 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 0.26 (5967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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: 0.261 AC: 39546 AN: 151808 Hom.: 5970 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0188

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.260 AC: 39533 AN: 151926 Hom.: 5967 Cov.: 32 AF XY: 0.257 AC XY: 19082 AN XY: 74240

African (AFR) AF: 0.135 AC: 5596 AN: 41456

American (AMR) AF: 0.246 AC: 3758 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.0186 AC: 96 AN: 5152

South Asian (SAS) AF: 0.206 AC: 992 AN: 4806

European-Finnish (FIN) AF: 0.298 AC: 3144 AN: 10534

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23808 AN: 67928

Other (OTH) AF: 0.285 AC: 600 AN: 2108

Alfa AF: 0.287 Hom.: 833

Bravo AF: 0.251

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.86
DANN	Benign	0.44
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs751160; hg19: chr10-100070040;