11-73601207-C-T

Position:

• chr11-73601207-C-T

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 0.781 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.806

Alfa AF: 0.816 Hom.: 69383

Bravo AF: 0.776

Asia WGS AF: 0.926 AC: 3219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10751226; hg19: chr11-73312252;