19-15046465-C-T

Variant names:

• chr19-15046465-C-T
• rs4808901
• ENST00000784685.1:n.340+6123G>A

Variant summary

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

The ENST00000784685.1(ENSG00000302149):​n.340+6123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,958 control chromosomes in the GnomAD database, including 12,532 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 0.40 (12532 hom., cov: 32)
• Consequence: ENSG00000302149 ENST00000784685.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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+6123G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61333 AN: 151840 Hom.: 12526 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.404 AC: 61362 AN: 151958 Hom.: 12532 Cov.: 32 AF XY: 0.402 AC XY: 29850 AN XY: 74242

African (AFR) AF: 0.352 AC: 14587 AN: 41430

American (AMR) AF: 0.358 AC: 5472 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3466

East Asian (EAS) AF: 0.389 AC: 2012 AN: 5172

South Asian (SAS) AF: 0.322 AC: 1549 AN: 4818

European-Finnish (FIN) AF: 0.485 AC: 5101 AN: 10520

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29630 AN: 67972

Other (OTH) AF: 0.412 AC: 869 AN: 2110

Alfa AF: 0.317 Hom.: 1095

Bravo AF: 0.395

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4808901; hg19: chr19-15157276;