rs7474896

Variant names:

• chr10-37693169-C-T
• rs7474896

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 0.111 in 152,150 control chromosomes in the GnomAD database, including 1,212 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 0.11 (1212 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.183 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: 0.111 AC: 16913 AN: 152032 Hom.: 1209 Cov.: 33

Gnomad AFR AF: 0.0357

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.0936

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.111 AC: 16918 AN: 152150 Hom.: 1212 Cov.: 33 AF XY: 0.111 AC XY: 8276 AN XY: 74386

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0675

Gnomad4 FIN AF: 0.0936

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.137

Alfa AF: 0.137 Hom.: 2285

Bravo AF: 0.119

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7474896; hg19: chr10-37982097;