rs2181184

Variant names:

• chr13-49696936-G-A
• rs2181184

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0905

Gnomad4 NFE AF: 0.0264

Gnomad4 OTH AF: 0.0994

Alfa AF: 0.0520 Hom.: 1144

Bravo AF: 0.127

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2181184; hg19: chr13-50271072;