11-13224675-T-G

Variant names:

• chr11-13224675-T-G
• rs12808129

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 0.346 in 152,086 control chromosomes in the GnomAD database, including 11,205 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 0.35 (11205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.346 AC: 52580 AN: 151966 Hom.: 11201 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.346 AC: 52592 AN: 152086 Hom.: 11205 Cov.: 32 AF XY: 0.350 AC XY: 26012 AN XY: 74324

African (AFR) AF: 0.0918 AC: 3808 AN: 41498

American (AMR) AF: 0.329 AC: 5022 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1801 AN: 5162

South Asian (SAS) AF: 0.475 AC: 2289 AN: 4816

European-Finnish (FIN) AF: 0.485 AC: 5119 AN: 10550

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31618 AN: 67998

Other (OTH) AF: 0.392 AC: 827 AN: 2112

Alfa AF: 0.427 Hom.: 45222

Bravo AF: 0.321

Asia WGS AF: 0.389 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.35
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs12808129; hg19: chr11-13246222;