chr2-5861950-C-A

Variant names:

• chr2-5861950-C-A
• rs2564023

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 0.119 in 152,178 control chromosomes in the GnomAD database, including 1,645 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 0.12 (1645 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 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: 0.119 AC: 18053 AN: 152060 Hom.: 1640 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.119 AC: 18076 AN: 152178 Hom.: 1645 Cov.: 33 AF XY: 0.123 AC XY: 9131 AN XY: 74388

African (AFR) AF: 0.154 AC: 6377 AN: 41492

American (AMR) AF: 0.179 AC: 2745 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0877 AC: 304 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2496 AN: 5166

South Asian (SAS) AF: 0.148 AC: 711 AN: 4818

European-Finnish (FIN) AF: 0.0521 AC: 553 AN: 10610

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0669 AC: 4547 AN: 68016

Other (OTH) AF: 0.120 AC: 252 AN: 2108

Alfa AF: 0.0685 Hom.: 252

Bravo AF: 0.132

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2564023; hg19: chr2-6002082;