11-116835452-T-G

Variant names:

• chr11-116835452-T-G
• rs12721026

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 0.051 in 152,368 control chromosomes in the GnomAD database, including 292 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 0.051 (292 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 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: 0.0511 AC: 7786 AN: 152250 Hom.: 292 Cov.: 33

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0510 AC: 7771 AN: 152368 Hom.: 292 Cov.: 33 AF XY: 0.0522 AC XY: 3888 AN XY: 74512

African (AFR) AF: 0.0128 AC: 534 AN: 41600

American (AMR) AF: 0.0396 AC: 606 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3472

East Asian (EAS) AF: 0.0499 AC: 259 AN: 5186

South Asian (SAS) AF: 0.109 AC: 526 AN: 4832

European-Finnish (FIN) AF: 0.0764 AC: 811 AN: 10622

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0664 AC: 4517 AN: 68024

Other (OTH) AF: 0.0477 AC: 101 AN: 2116

Alfa AF: 0.0569 Hom.: 36

Bravo AF: 0.0463

Asia WGS AF: 0.0830 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12721026; hg19: chr11-116706168;