rs2537859

Positions:

• chr4-54616651-C-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 0.501 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54616651C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.460

Alfa AF: 0.435 Hom.: 16804

Bravo AF: 0.509

Asia WGS AF: 0.532 AC: 1849 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	0.080
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2537859; hg19: chr4-55482818;