ENST00000690022.2:n.289-1702C>G

Variant names:

• chr7-128223242-G-C
• rs4731420
• ENST00000690022.2:n.289-1702C>G

Variant summary

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

The ENST00000690022.2(ENSG00000289434):​n.289-1702C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,074 control chromosomes in the GnomAD database, including 2,884 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 0.19 (2884 hom., cov: 31)
• Consequence: ENSG00000289434 ENST00000690022.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 11 publications found

Genes affected

ENSG00000289434 (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 (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901744	XR_007060516.1	n.781-791G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289434	ENST00000690022.2	n.289-1702C>G		intron_variant	Intron 2 of 2
ENSG00000289434	ENST00000692614.3	n.528-1702C>G		intron_variant	Intron 2 of 2
ENSG00000292309	ENST00000710955.1	n.836-791G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29354 AN: 151956 Hom.: 2884 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.193 AC: 29364 AN: 152074 Hom.: 2884 Cov.: 31 AF XY: 0.191 AC XY: 14231 AN XY: 74350

African (AFR) AF: 0.237 AC: 9833 AN: 41454

American (AMR) AF: 0.155 AC: 2368 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3468

East Asian (EAS) AF: 0.117 AC: 607 AN: 5178

South Asian (SAS) AF: 0.152 AC: 730 AN: 4808

European-Finnish (FIN) AF: 0.175 AC: 1848 AN: 10590

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12664 AN: 67972

Other (OTH) AF: 0.200 AC: 423 AN: 2116

Alfa AF: 0.113 Hom.: 185

Bravo AF: 0.195

Asia WGS AF: 0.121 AC: 422 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	6.5
DANN	Benign	0.65
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs4731420; hg19: chr7-127863295;