11-13272432-A-T

Variant names:

• chr11-13272432-A-T
• rs7109016

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 0.62 in 152,072 control chromosomes in the GnomAD database, including 30,096 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 0.62 (30096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.620 AC: 94161 AN: 151954 Hom.: 30063 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.620 AC: 94247 AN: 152072 Hom.: 30096 Cov.: 32 AF XY: 0.622 AC XY: 46248 AN XY: 74340

African (AFR) AF: 0.463 AC: 19193 AN: 41448

American (AMR) AF: 0.618 AC: 9454 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2293 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2772 AN: 5174

South Asian (SAS) AF: 0.637 AC: 3072 AN: 4824

European-Finnish (FIN) AF: 0.723 AC: 7636 AN: 10566

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.702 AC: 47746 AN: 67986

Other (OTH) AF: 0.640 AC: 1353 AN: 2114

Alfa AF: 0.573 Hom.: 1859

Bravo AF: 0.607

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.71
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs7109016; hg19: chr11-13293979;