19-15032397-C-A

Variant names:

• chr19-15032397-C-A
• rs8110862
• ENST00000784685.1:n.340+20191G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000784685.1(ENSG00000302149):​n.340+20191G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302149 ENST00000784685.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 3 publications found

Genes affected

ENSG00000302149 (HGNC:):

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302149	ENST00000784685.1	n.340+20191G>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.653 AC: 27034 AN: 41410

American (AMR) AF: 0.754 AC: 11511 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2704 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3347 AN: 5142

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4812

European-Finnish (FIN) AF: 0.637 AC: 6697 AN: 10510

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45652 AN: 67944

Other (OTH) AF: 0.701 AC: 1478 AN: 2108

Alfa AF: 0.678 Hom.: 4545

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs8110862; hg19: chr19-15143208;