11-73766000-C-T

Variant names:

• chr11-73766000-C-T
• rs1723838

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 0.0851 in 152,238 control chromosomes in the GnomAD database, including 737 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 0.085 (737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.0851 AC: 12949 AN: 152120 Hom.: 737 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.0851 AC: 12952 AN: 152238 Hom.: 737 Cov.: 32 AF XY: 0.0815 AC XY: 6065 AN XY: 74430

African (AFR) AF: 0.164 AC: 6800 AN: 41534

American (AMR) AF: 0.0591 AC: 904 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4828

European-Finnish (FIN) AF: 0.0270 AC: 286 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4179 AN: 68028

Other (OTH) AF: 0.0915 AC: 193 AN: 2110

Alfa AF: 0.0775 Hom.: 867

Bravo AF: 0.0908

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.92
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1723838; hg19: chr11-73477045;