rs3814758

Variant names:

• chr11-119347108-A-G
• rs3814758

Your query was ambiguous. Multiple possible variants found:

• chr11-119347108-A-G
• chr11-119347108-A-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 0.589 in 152,032 control chromosomes in the GnomAD database, including 26,504 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 0.59 (26504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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: 0.589 AC: 89416 AN: 151912 Hom.: 26475 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.589 AC: 89491 AN: 152032 Hom.: 26504 Cov.: 32 AF XY: 0.591 AC XY: 43933 AN XY: 74304

African (AFR) AF: 0.566 AC: 23436 AN: 41434

American (AMR) AF: 0.585 AC: 8939 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1993 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3825 AN: 5166

South Asian (SAS) AF: 0.676 AC: 3260 AN: 4826

European-Finnish (FIN) AF: 0.543 AC: 5744 AN: 10578

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40144 AN: 67952

Other (OTH) AF: 0.612 AC: 1292 AN: 2110

Alfa AF: 0.583 Hom.: 3972

Bravo AF: 0.594

Asia WGS AF: 0.718 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.7
DANN	Benign	0.81
PhyloP100		-0.48
PromoterAI		-0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3814758; hg19: chr11-119217818;