5-19393794-C-T

Position:

• chr5-19393794-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 0.319 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;