rs2201544

Variant names:

• chr4-81008523-G-A
• rs2201544

Your query was ambiguous. Multiple possible variants found:

• chr4-81008523-G-A
• chr4-81008523-G-C
• chr4-81008523-G-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 0.816 in 152,148 control chromosomes in the GnomAD database, including 51,867 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 0.82 (51867 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.817 AC: 124139 AN: 152030 Hom.: 51838 Cov.: 31

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.816 AC: 124214 AN: 152148 Hom.: 51867 Cov.: 31 AF XY: 0.821 AC XY: 61046 AN XY: 74394

African (AFR) AF: 0.628 AC: 26020 AN: 41466

American (AMR) AF: 0.876 AC: 13382 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2498 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4862 AN: 5170

South Asian (SAS) AF: 0.871 AC: 4198 AN: 4822

European-Finnish (FIN) AF: 0.919 AC: 9745 AN: 10608

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60760 AN: 68010

Other (OTH) AF: 0.818 AC: 1725 AN: 2110

Alfa AF: 0.848 Hom.: 7203

Bravo AF: 0.804

Asia WGS AF: 0.886 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.34
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2201544; hg19: chr4-81929677;