rs11184981

Variant names:

• chr1-106756641-T-A
• rs11184981

Your query was ambiguous. Multiple possible variants found:

• chr1-106756641-T-A
• chr1-106756641-T-C

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 0.173 in 152,006 control chromosomes in the GnomAD database, including 2,569 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 0.17 (2569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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: 0.173 AC: 26233 AN: 151888 Hom.: 2562 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.173 AC: 26264 AN: 152006 Hom.: 2569 Cov.: 32 AF XY: 0.173 AC XY: 12858 AN XY: 74326

African (AFR) AF: 0.241 AC: 10005 AN: 41464

American (AMR) AF: 0.154 AC: 2352 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1457 AN: 5132

South Asian (SAS) AF: 0.193 AC: 928 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10582

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9153 AN: 67956

Other (OTH) AF: 0.155 AC: 327 AN: 2110

Alfa AF: 0.152 Hom.: 236

Bravo AF: 0.180

Asia WGS AF: 0.244 AC: 847 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.73
DANN	Benign	0.42
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs11184981; hg19: chr1-107299263;