rs10902096

Variant names:

• chr11-1123373-T-C
• rs10902096

Your query was ambiguous. Multiple possible variants found:

• chr11-1123373-T-C
• chr11-1123373-T-G

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 0.722 in 151,776 control chromosomes in the GnomAD database, including 40,904 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 0.72 (40904 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 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: 0.722 AC: 109566 AN: 151656 Hom.: 40912 Cov.: 30

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.722 AC: 109580 AN: 151776 Hom.: 40904 Cov.: 30 AF XY: 0.717 AC XY: 53218 AN XY: 74212

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.736

Alfa AF: 0.794 Hom.: 12994

Bravo AF: 0.703

Asia WGS AF: 0.586 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.74
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10902096; hg19: chr11-1117281;