rs2561858

Positions:

• chr5-5859309-A-C
• chr5-5859309-A-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 0.674 in 152,042 control chromosomes in the GnomAD database, including 35,348 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 0.67 (35348 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5859309A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102323 AN: 151924 Hom.: 35301 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.674 AC: 102420 AN: 152042 Hom.: 35348 Cov.: 32 AF XY: 0.667 AC XY: 49562 AN XY: 74292

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.656

Alfa AF: 0.632 Hom.: 37918

Bravo AF: 0.668

Asia WGS AF: 0.600 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2561858; hg19: chr5-5859422;