rs2942321

Variant names:

• chr5-19329361-G-A
• rs2942321

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 0.336 in 151,798 control chromosomes in the GnomAD database, including 8,952 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 0.34 (8952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 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: 0.336 AC: 51029 AN: 151680 Hom.: 8952 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0946

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.336 AC: 51056 AN: 151798 Hom.: 8952 Cov.: 33 AF XY: 0.335 AC XY: 24854 AN XY: 74164

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.0943

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.324

Alfa AF: 0.369 Hom.: 1792

Bravo AF: 0.337

Asia WGS AF: 0.227 AC: 788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2942321; hg19: chr5-19329470;