chr19-18021731-T-C

Variant names:

• chr19-18021731-T-C
• rs12984174
• ENST00000783902.1:n.245-3668A>G

Variant summary

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

The ENST00000783902.1(ENSG00000302080):​n.245-3668A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,854 control chromosomes in the GnomAD database, including 1,085 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 0.11 (1085 hom., cov: 30)
• Consequence: ENSG00000302080 ENST00000783902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750
• Publications: 10 publications found

Genes affected

ENSG00000302080 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783902.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302080	ENST00000783902.1		n.245-3668A>G		intron	N/A
	ENSG00000302080	ENST00000783903.1		n.176-5801A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17392 AN: 151736 Hom.: 1081 Cov.: 30

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.115 AC: 17407 AN: 151854 Hom.: 1085 Cov.: 30 AF XY: 0.114 AC XY: 8455 AN XY: 74214

African (AFR) AF: 0.107 AC: 4444 AN: 41378

American (AMR) AF: 0.0942 AC: 1436 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3466

East Asian (EAS) AF: 0.0789 AC: 407 AN: 5160

South Asian (SAS) AF: 0.112 AC: 537 AN: 4806

European-Finnish (FIN) AF: 0.124 AC: 1315 AN: 10566

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8252 AN: 67922

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.116 Hom.: 3211

Bravo AF: 0.110

Asia WGS AF: 0.125 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.66
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs12984174; hg19: chr19-18132540;