ENST00000722984.1:n.218+3789G>A

Variant names:

• chr17-71493932-G-A
• rs9907236
• ENST00000722984.1:n.218+3789G>A

Variant summary

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

The ENST00000722984.1(ENSG00000294342):​n.218+3789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0416 in 152,228 control chromosomes in the GnomAD database, including 235 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 0.042 (235 hom., cov: 32)
• Consequence: ENSG00000294342 ENST00000722984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 6 publications found

Genes affected

ENSG00000294342 (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 (EAS) allele frequency at 95% confidence interval = 0.119 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
ENSG00000294342	ENST00000722984.1	n.218+3789G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6316 AN: 152112 Hom.: 235 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0416 AC: 6326 AN: 152228 Hom.: 235 Cov.: 32 AF XY: 0.0424 AC XY: 3155 AN XY: 74418

African (AFR) AF: 0.0862 AC: 3580 AN: 41544

American (AMR) AF: 0.0226 AC: 346 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.127 AC: 658 AN: 5182

South Asian (SAS) AF: 0.111 AC: 535 AN: 4814

European-Finnish (FIN) AF: 0.00386 AC: 41 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0144 AC: 978 AN: 68016

Other (OTH) AF: 0.0342 AC: 72 AN: 2108

Alfa AF: 0.0225 Hom.: 77

Bravo AF: 0.0438

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs9907236; hg19: chr17-69490073;