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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.359 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

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.338

Alfa AF: 0.385 Hom.: 23760

Bravo AF: 0.355

Asia WGS AF: 0.461 AC: 1602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1119911; hg19: chr13-32081769;