rs2213041

Variant names:

• chr4-99326194-C-A
• rs2213041

Your query was ambiguous. Multiple possible variants found:

• chr4-99326194-C-A
• chr4-99326194-C-T

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 0.127 in 152,188 control chromosomes in the GnomAD database, including 1,518 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 0.13 (1518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 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: 0.127 AC: 19272 AN: 152070 Hom.: 1510 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.127 AC: 19286 AN: 152188 Hom.: 1518 Cov.: 32 AF XY: 0.128 AC XY: 9514 AN XY: 74392

African (AFR) AF: 0.0387 AC: 1609 AN: 41552

American (AMR) AF: 0.146 AC: 2226 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3470

East Asian (EAS) AF: 0.0611 AC: 315 AN: 5156

South Asian (SAS) AF: 0.171 AC: 827 AN: 4826

European-Finnish (FIN) AF: 0.199 AC: 2103 AN: 10590

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11564 AN: 68008

Other (OTH) AF: 0.118 AC: 249 AN: 2116

Alfa AF: 0.147 Hom.: 3776

Bravo AF: 0.120

Asia WGS AF: 0.143 AC: 494 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.51
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2213041; hg19: chr4-100247351;