rs1384936

chr19-5423632-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 0.581 in 151,828 control chromosomes in the GnomAD database, including 25,892 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 0.58 (25892 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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 (EAS) allele frequency at 95% confidence interval = 0.64 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: 0.581 AC: 88206 AN: 151710 Hom.: 25872 Cov.: 30

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.581 AC: 88275 AN: 151828 Hom.: 25892 Cov.: 30 AF XY: 0.583 AC XY: 43266 AN XY: 74186

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.591

Alfa AF: 0.606 Hom.: 36885

Bravo AF: 0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.14
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1384936; hg19: chr19-5423643;