rs2537859

Variant names:

• chr4-54616651-C-T
• rs2537859

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 0.501 in 150,814 control chromosomes in the GnomAD database, including 19,917 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 0.50 (19917 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75450 AN: 150696 Hom.: 19875 Cov.: 29

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.501 AC: 75549 AN: 150814 Hom.: 19917 Cov.: 29 AF XY: 0.502 AC XY: 36979 AN XY: 73658

African (AFR) AF: 0.654 AC: 26812 AN: 40994

American (AMR) AF: 0.523 AC: 7909 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 890 AN: 3452

East Asian (EAS) AF: 0.431 AC: 2197 AN: 5092

South Asian (SAS) AF: 0.483 AC: 2291 AN: 4746

European-Finnish (FIN) AF: 0.488 AC: 5085 AN: 10430

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29078 AN: 67678

Other (OTH) AF: 0.460 AC: 964 AN: 2094

Alfa AF: 0.458 Hom.: 27278

Bravo AF: 0.509

Asia WGS AF: 0.532 AC: 1849 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	0.080
DANN	Benign	0.13
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2537859; hg19: chr4-55482818;