11-73601207-C-T

Variant names:

• chr11-73601207-C-T
• rs10751226

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 0.781 in 152,042 control chromosomes in the GnomAD database, including 47,243 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 0.78 (47243 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.781 AC: 118723 AN: 151924 Hom.: 47209 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.781 AC: 118811 AN: 152042 Hom.: 47243 Cov.: 31 AF XY: 0.787 AC XY: 58488 AN XY: 74330

African (AFR) AF: 0.625 AC: 25862 AN: 41402

American (AMR) AF: 0.853 AC: 13034 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2824 AN: 3470

East Asian (EAS) AF: 0.989 AC: 5131 AN: 5186

South Asian (SAS) AF: 0.897 AC: 4323 AN: 4822

European-Finnish (FIN) AF: 0.849 AC: 8989 AN: 10584

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55862 AN: 67984

Other (OTH) AF: 0.806 AC: 1700 AN: 2110

Alfa AF: 0.810 Hom.: 161132

Bravo AF: 0.776

Asia WGS AF: 0.926 AC: 3219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.75
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs10751226; hg19: chr11-73312252;