11-112797016-A-T

Variant names:

• chr11-112797016-A-T
• rs321146

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 0.37 in 152,048 control chromosomes in the GnomAD database, including 10,897 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 0.37 (10897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56198 AN: 151928 Hom.: 10896 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.370 AC: 56229 AN: 152048 Hom.: 10897 Cov.: 32 AF XY: 0.380 AC XY: 28262 AN XY: 74320

African (AFR) AF: 0.327 AC: 13549 AN: 41448

American (AMR) AF: 0.436 AC: 6672 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3474 AN: 5152

South Asian (SAS) AF: 0.522 AC: 2515 AN: 4816

European-Finnish (FIN) AF: 0.412 AC: 4358 AN: 10572

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23160 AN: 67980

Other (OTH) AF: 0.385 AC: 814 AN: 2114

Alfa AF: 0.328 Hom.: 997

Bravo AF: 0.370

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs321146; hg19: chr11-112667739;