ENST00000784484.1:n.295+7999T>G

Variant names:

• chr20-11528332-A-C
• rs4814019
• ENST00000784484.1:n.295+7999T>G

Variant summary

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

The ENST00000784484.1(ENSG00000282478):​n.295+7999T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,952 control chromosomes in the GnomAD database, including 10,920 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 0.37 (10920 hom., cov: 32)
• Consequence: ENSG00000282478 ENST00000784484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806
• Publications: 7 publications found

Genes affected

ENSG00000282478 (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 (AFR) allele frequency at 95% confidence interval = 0.486 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
ENSG00000282478	ENST00000784484.1	n.295+7999T>G		intron_variant	Intron 1 of 2
ENSG00000282478	ENST00000784485.1	n.152+7999T>G		intron_variant	Intron 1 of 2
ENSG00000282478	ENST00000784486.1	n.185+13155T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56331 AN: 151834 Hom.: 10916 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.371 AC: 56374 AN: 151952 Hom.: 10920 Cov.: 32 AF XY: 0.372 AC XY: 27603 AN XY: 74258

African (AFR) AF: 0.492 AC: 20370 AN: 41400

American (AMR) AF: 0.298 AC: 4550 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1182 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2261 AN: 5154

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4283 AN: 10544

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21224 AN: 67970

Other (OTH) AF: 0.377 AC: 795 AN: 2110

Alfa AF: 0.331 Hom.: 26461

Bravo AF: 0.372

Asia WGS AF: 0.361 AC: 1252 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	1.9
DANN	Benign	0.61
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs4814019; hg19: chr20-11508980;