rs1119911

Variant names:

• chr13-31507632-G-A
• rs1119911

Your query was ambiguous. Multiple possible variants found:

• chr13-31507632-G-A
• chr13-31507632-G-C
• chr13-31507632-G-T

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 0.358 in 151,700 control chromosomes in the GnomAD database, including 10,156 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 0.36 (10156 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.537 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: 0.359 AC: 54362 AN: 151582 Hom.: 10152 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.358 AC: 54382 AN: 151700 Hom.: 10156 Cov.: 31 AF XY: 0.359 AC XY: 26579 AN XY: 74128

African (AFR) AF: 0.283 AC: 11711 AN: 41316

American (AMR) AF: 0.350 AC: 5333 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3462

East Asian (EAS) AF: 0.554 AC: 2855 AN: 5156

South Asian (SAS) AF: 0.515 AC: 2473 AN: 4802

European-Finnish (FIN) AF: 0.339 AC: 3558 AN: 10504

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 25989 AN: 67918

Other (OTH) AF: 0.338 AC: 715 AN: 2114

Alfa AF: 0.378 Hom.: 35878

Bravo AF: 0.355

Asia WGS AF: 0.461 AC: 1602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.66
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1119911; hg19: chr13-32081769;