5-19393794-C-T

Variant names:

• chr5-19393794-C-T
• rs2942329

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 0.319 in 151,832 control chromosomes in the GnomAD database, including 8,428 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 0.32 (8428 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

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 = 0.42 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: 0.320 AC: 48489 AN: 151714 Hom.: 8431 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0908

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.319 AC: 48503 AN: 151832 Hom.: 8428 Cov.: 31 AF XY: 0.320 AC XY: 23714 AN XY: 74196

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0906

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.300

Alfa AF: 0.361 Hom.: 14822

Bravo AF: 0.318

Asia WGS AF: 0.226 AC: 784 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2942329; hg19: chr5-19393903;