rs11118346

Variant names:

• chr1-219570377-C-T
• rs11118346

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 0.389 in 151,768 control chromosomes in the GnomAD database, including 13,214 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 0.39 (13214 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 45 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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: 0.389 AC: 59064 AN: 151650 Hom.: 13215 Cov.: 30

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.389 AC: 59086 AN: 151768 Hom.: 13214 Cov.: 30 AF XY: 0.396 AC XY: 29380 AN XY: 74118

African (AFR) AF: 0.167 AC: 6910 AN: 41432

American (AMR) AF: 0.360 AC: 5493 AN: 15268

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

East Asian (EAS) AF: 0.648 AC: 3320 AN: 5122

South Asian (SAS) AF: 0.580 AC: 2787 AN: 4808

European-Finnish (FIN) AF: 0.504 AC: 5277 AN: 10472

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31837 AN: 67880

Other (OTH) AF: 0.425 AC: 895 AN: 2108

Alfa AF: 0.447 Hom.: 50052

Bravo AF: 0.363

Asia WGS AF: 0.543 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11118346; hg19: chr1-219743719;