chr5-5859309-A-C

Variant names:

• chr5-5859309-A-C
• rs2561858

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 0.674 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.803 AC: 33307 AN: 41456

American (AMR) AF: 0.526 AC: 8038 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1871 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3110 AN: 5166

South Asian (SAS) AF: 0.476 AC: 2289 AN: 4812

European-Finnish (FIN) AF: 0.696 AC: 7356 AN: 10566

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44371 AN: 67982

Other (OTH) AF: 0.656 AC: 1385 AN: 2112

Alfa AF: 0.638 Hom.: 49962

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
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs2561858; hg19: chr5-5859422;