rs2942325

Positions:

• chr5-19398951-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 0.367 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.0988

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.363

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2942325; hg19: chr5-19399060;