chr11-13239843-C-T

Variant names:

• chr11-13239843-C-T
• rs11607529

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 0.397 in 152,034 control chromosomes in the GnomAD database, including 14,157 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 0.40 (14157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.527 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: 0.397 AC: 60277 AN: 151916 Hom.: 14160 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.397 AC: 60292 AN: 152034 Hom.: 14157 Cov.: 32 AF XY: 0.397 AC XY: 29479 AN XY: 74304

African (AFR) AF: 0.142 AC: 5894 AN: 41492

American (AMR) AF: 0.378 AC: 5774 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1711 AN: 5184

South Asian (SAS) AF: 0.483 AC: 2326 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5019 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36146 AN: 67948

Other (OTH) AF: 0.456 AC: 963 AN: 2110

Alfa AF: 0.501 Hom.: 33150

Bravo AF: 0.377

Asia WGS AF: 0.395 AC: 1374 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	2.5
DANN	Benign	0.45
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs11607529; hg19: chr11-13261390;