19-15032397-C-A

Position:

• chr19-15032397-C-A

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 0.672 in 151,866 control chromosomes in the GnomAD database, including 34,416 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 0.67 (34416 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.743 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: 0.672 AC: 101921 AN: 151748 Hom.: 34369 Cov.: 30

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.672 AC: 102020 AN: 151866 Hom.: 34416 Cov.: 30 AF XY: 0.672 AC XY: 49833 AN XY: 74186

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.701

Alfa AF: 0.679 Hom.: 4380

Bravo AF: 0.681

Asia WGS AF: 0.655 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8110862; hg19: chr19-15143208;