19-15640081-A-G

Position:

• chr19-15640081-A-G

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 0.456 in 151,860 control chromosomes in the GnomAD database, including 16,614 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 0.46 (16614 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69246 AN: 151742 Hom.: 16606 Cov.: 30

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.456 AC: 69285 AN: 151860 Hom.: 16614 Cov.: 30 AF XY: 0.452 AC XY: 33567 AN XY: 74220

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.473

Alfa AF: 0.513 Hom.: 19027

Bravo AF: 0.446

Asia WGS AF: 0.309 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3794987; hg19: chr19-15750891;