rs2181184

Variant names:

• chr13-49696936-G-A
• rs2181184

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 0.115 in 152,180 control chromosomes in the GnomAD database, including 2,056 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 (2056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.115 AC: 17457 AN: 152060 Hom.: 2048 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.115 AC: 17496 AN: 152180 Hom.: 2056 Cov.: 32 AF XY: 0.121 AC XY: 9037 AN XY: 74402

African (AFR) AF: 0.202 AC: 8386 AN: 41490

American (AMR) AF: 0.143 AC: 2184 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3006 AN: 5164

South Asian (SAS) AF: 0.137 AC: 661 AN: 4824

European-Finnish (FIN) AF: 0.0905 AC: 960 AN: 10612

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0264 AC: 1793 AN: 68008

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0621 Hom.: 3388

Bravo AF: 0.127

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2181184; hg19: chr13-50271072;