rs694428

Variant names:

• chr9-117850980-G-A
• rs694428
• ENST00000697666.1:c.*45+2825G>A

Variant summary

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

The ENST00000697666.1(ENSG00000285082):​c.*45+2825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,982 control chromosomes in the GnomAD database, including 2,757 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 0.15 (2757 hom., cov: 31)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 2 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697666.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285082	ENST00000697666.1		c.*45+2825G>A		intron	N/A	ENSP00000513391.1
	ENSG00000285082	ENST00000646089.2		c.*16+2825G>A		intron	N/A	ENSP00000496197.1
	ENSG00000285082	ENST00000697637.1		c.*16+2825G>A		intron	N/A	ENSP00000513367.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23135 AN: 151866 Hom.: 2751 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.153 AC: 23184 AN: 151982 Hom.: 2757 Cov.: 31 AF XY: 0.154 AC XY: 11430 AN XY: 74276

African (AFR) AF: 0.298 AC: 12339 AN: 41392

American (AMR) AF: 0.217 AC: 3321 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1662 AN: 5156

South Asian (SAS) AF: 0.117 AC: 563 AN: 4818

European-Finnish (FIN) AF: 0.0530 AC: 560 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0598 AC: 4063 AN: 67986

Other (OTH) AF: 0.133 AC: 280 AN: 2104

Alfa AF: 0.0942 Hom.: 4588

Bravo AF: 0.174

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.44
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs694428; hg19: chr9-120613258;