rs11838472

Variant names:

• chr13-73167012-C-T
• rs11838472

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 0.119 in 152,130 control chromosomes in the GnomAD database, including 1,799 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 0.12 (1799 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.119 AC: 18155 AN: 152012 Hom.: 1799 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.119 AC: 18171 AN: 152130 Hom.: 1799 Cov.: 31 AF XY: 0.128 AC XY: 9538 AN XY: 74364

African (AFR) AF: 0.229 AC: 9487 AN: 41486

American (AMR) AF: 0.125 AC: 1906 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1524 AN: 5188

South Asian (SAS) AF: 0.177 AC: 853 AN: 4816

European-Finnish (FIN) AF: 0.156 AC: 1651 AN: 10560

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0364 AC: 2474 AN: 68016

Other (OTH) AF: 0.0924 AC: 195 AN: 2110

Alfa AF: 0.0637 Hom.: 1940

Bravo AF: 0.120

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11838472; hg19: chr13-73741149;