19-41853387-C-A

Variant names:

• chr19-41853387-C-A
• rs4803512

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.175 AC: 7267 AN: 41482

American (AMR) AF: 0.489 AC: 7461 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2252 AN: 5150

South Asian (SAS) AF: 0.558 AC: 2684 AN: 4812

European-Finnish (FIN) AF: 0.481 AC: 5081 AN: 10562

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35281 AN: 67954

Other (OTH) AF: 0.452 AC: 954 AN: 2112

Alfa AF: 0.484 Hom.: 9849

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4803512; hg19: chr19-42357455;