rs17110453

Variant names:

• chr10-95069772-A-C
• rs17110453

Your query was ambiguous. Multiple possible variants found:

• chr10-95069772-A-C
• chr10-95069772-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.119 in 152,164 control chromosomes in the GnomAD database, including 1,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.12 (1433 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 10-95069772-A-C is Benign according to our data. Variant chr10-95069772-A-C is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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: 0.119 AC: 18028 AN: 152046 Hom.: 1426 Cov.: 33

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.119 AC: 18035 AN: 152164 Hom.: 1433 Cov.: 33 AF XY: 0.125 AC XY: 9275 AN XY: 74390

Gnomad4 AFR AF: 0.0285

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.132

Alfa AF: 0.137 Hom.: 1776

Bravo AF: 0.109

Asia WGS AF: 0.291 AC: 1006 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17110453; hg19: chr10-96829529;