chr19-15040907-T-C

Variant names:

• chr19-15040907-T-C
• rs714920
• ENST00000784685.1:n.340+11681A>G

Variant summary

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

The ENST00000784685.1(ENSG00000302149):​n.340+11681A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,970 control chromosomes in the GnomAD database, including 13,865 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 (13865 hom., cov: 30)
• Consequence: ENSG00000302149 ENST00000784685.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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+11681A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63789 AN: 151852 Hom.: 13860 Cov.: 30

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.420 AC: 63820 AN: 151970 Hom.: 13865 Cov.: 30 AF XY: 0.417 AC XY: 30965 AN XY: 74254

African (AFR) AF: 0.366 AC: 15153 AN: 41444

American (AMR) AF: 0.375 AC: 5725 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3466

East Asian (EAS) AF: 0.341 AC: 1765 AN: 5170

South Asian (SAS) AF: 0.330 AC: 1591 AN: 4828

European-Finnish (FIN) AF: 0.477 AC: 5037 AN: 10552

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31317 AN: 67934

Other (OTH) AF: 0.431 AC: 910 AN: 2110

Alfa AF: 0.453 Hom.: 70801

Bravo AF: 0.415

Asia WGS AF: 0.379 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs714920; hg19: chr19-15151718;