rs2942337

Variant names:

• chr5-19351242-T-C
• rs2942337

Your query was ambiguous. Multiple possible variants found:

• chr5-19351242-T-C
• chr5-19351242-T-G

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 0.45 in 151,914 control chromosomes in the GnomAD database, including 15,704 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 0.45 (15704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 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: 0.450 AC: 68267 AN: 151796 Hom.: 15697 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.450 AC: 68312 AN: 151914 Hom.: 15704 Cov.: 32 AF XY: 0.451 AC XY: 33466 AN XY: 74240

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.441

Alfa AF: 0.461 Hom.: 1963

Bravo AF: 0.446

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2942337; hg19: chr5-19351351;