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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.817 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

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.818

Alfa AF: 0.857 Hom.: 7054

Bravo AF: 0.804

Asia WGS AF: 0.886 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2201544; hg19: chr4-81929677;