3-113711752-T-G

Variant names:

• chr3-113711752-T-G
• rs11711311

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 0.333 in 152,034 control chromosomes in the GnomAD database, including 8,598 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 0.33 (8598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50664 AN: 151916 Hom.: 8596 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.333 AC: 50675 AN: 152034 Hom.: 8598 Cov.: 32 AF XY: 0.334 AC XY: 24794 AN XY: 74306

African (AFR) AF: 0.317 AC: 13133 AN: 41482

American (AMR) AF: 0.246 AC: 3755 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1877 AN: 5178

South Asian (SAS) AF: 0.208 AC: 1006 AN: 4828

European-Finnish (FIN) AF: 0.451 AC: 4765 AN: 10556

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24168 AN: 67922

Other (OTH) AF: 0.303 AC: 640 AN: 2110

Alfa AF: 0.293 Hom.: 2306

Bravo AF: 0.319

Asia WGS AF: 0.253 AC: 877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.81
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs11711311; hg19: chr3-113430599;