rs398426

chr19-33830353-G-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 0.23 in 151,942 control chromosomes in the GnomAD database, including 4,628 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 0.23 (4628 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.349 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: 0.230 AC: 34925 AN: 151824 Hom.: 4628 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.230 AC: 34922 AN: 151942 Hom.: 4628 Cov.: 31 AF XY: 0.235 AC XY: 17466 AN XY: 74250

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.232

Alfa AF: 0.263 Hom.: 4023

Bravo AF: 0.229

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	2.2
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs398426; hg19: chr19-34321258;