rs2942325

Variant names:

• chr5-19398951-C-T
• rs2942325

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 0.367 in 151,708 control chromosomes in the GnomAD database, including 11,263 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 0.37 (11263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.483 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: 0.367 AC: 55686 AN: 151590 Hom.: 11260 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.406

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.367 AC: 55701 AN: 151708 Hom.: 11263 Cov.: 32 AF XY: 0.365 AC XY: 27090 AN XY: 74124

African (AFR) AF: 0.224 AC: 9286 AN: 41398

American (AMR) AF: 0.493 AC: 7500 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3468

East Asian (EAS) AF: 0.0988 AC: 508 AN: 5144

South Asian (SAS) AF: 0.354 AC: 1703 AN: 4816

European-Finnish (FIN) AF: 0.384 AC: 4038 AN: 10520

Middle Eastern (MID) AF: 0.427 AC: 122 AN: 286

European-Non Finnish (NFE) AF: 0.440 AC: 29817 AN: 67838

Other (OTH) AF: 0.363 AC: 764 AN: 2106

Alfa AF: 0.406 Hom.: 1461

Bravo AF: 0.367

Asia WGS AF: 0.263 AC: 906 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.21
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2942325; hg19: chr5-19399060;