rs4803512

chr19-41853387-C-Achr19-41853387-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 0.418 in 152,000 control chromosomes in the GnomAD database, including 15,097 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 0.42 (15097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 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: 0.419 AC: 63589 AN: 151880 Hom.: 15096 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.418 AC: 63598 AN: 152000 Hom.: 15097 Cov.: 32 AF XY: 0.420 AC XY: 31213 AN XY: 74302

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.452

Alfa AF: 0.481 Hom.: 8818

Bravo AF: 0.405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803512; hg19: chr19-42357455;