rs2942321

Variant names:

• chr5-19329361-G-A
• rs2942321

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 0.336 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.279 AC: 11551 AN: 41400

American (AMR) AF: 0.432 AC: 6590 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3468

East Asian (EAS) AF: 0.0943 AC: 487 AN: 5166

South Asian (SAS) AF: 0.288 AC: 1389 AN: 4818

European-Finnish (FIN) AF: 0.354 AC: 3720 AN: 10516

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25160 AN: 67868

Other (OTH) AF: 0.324 AC: 683 AN: 2110

Alfa AF: 0.367 Hom.: 1834

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2942321; hg19: chr5-19329470;