chr11-1123373-T-C

Variant names:

• chr11-1123373-T-C
• rs10902096

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 0.722 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.543 AC: 22420 AN: 41252

American (AMR) AF: 0.639 AC: 9757 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2888 AN: 3466

East Asian (EAS) AF: 0.701 AC: 3598 AN: 5132

South Asian (SAS) AF: 0.617 AC: 2961 AN: 4796

European-Finnish (FIN) AF: 0.840 AC: 8880 AN: 10572

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56435 AN: 67982

Other (OTH) AF: 0.736 AC: 1555 AN: 2112

Alfa AF: 0.791 Hom.: 15622

Bravo AF: 0.703

Asia WGS AF: 0.586 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.74
DANN	Benign	0.73
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10902096; hg19: chr11-1117281;