rs11184708

Variant names:

• chr1-105887665-A-T
• rs11184708

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 0.114 in 152,146 control chromosomes in the GnomAD database, including 1,122 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 0.11 (1122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17357 AN: 152028 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.0904

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.114 AC: 17379 AN: 152146 Hom.: 1122 Cov.: 32 AF XY: 0.117 AC XY: 8674 AN XY: 74366

African (AFR) AF: 0.0904 AC: 3753 AN: 41522

American (AMR) AF: 0.152 AC: 2319 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1244 AN: 5156

South Asian (SAS) AF: 0.177 AC: 852 AN: 4812

European-Finnish (FIN) AF: 0.0885 AC: 936 AN: 10580

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7351 AN: 68010

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.110 Hom.: 116

Bravo AF: 0.115

Asia WGS AF: 0.187 AC: 652 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.42
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs11184708; hg19: chr1-106430287;