ENST00000725701.1:n.125+2898G>C

Variant names:

• chr1-22166394-G-C
• rs3920498
• ENST00000725701.1:n.125+2898G>C

Variant summary

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

The ENST00000725701.1(ENSG00000294752):​n.125+2898G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,180 control chromosomes in the GnomAD database, including 3,195 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 0.20 (3195 hom., cov: 32)
• Consequence: ENSG00000294752 ENST00000725701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 29 publications found

Genes affected

ENSG00000294752 (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 = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725701.1. 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
	ENSG00000294752	ENST00000725701.1		n.125+2898G>C		intron	N/A
	ENSG00000294752	ENST00000725702.1		n.125+2898G>C		intron	N/A
	ENSG00000294752	ENST00000725703.1		n.108+2898G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29874 AN: 152060 Hom.: 3186 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.197 AC: 29910 AN: 152180 Hom.: 3195 Cov.: 32 AF XY: 0.201 AC XY: 14979 AN XY: 74402

African (AFR) AF: 0.163 AC: 6772 AN: 41516

American (AMR) AF: 0.217 AC: 3327 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2353 AN: 5168

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4826

European-Finnish (FIN) AF: 0.210 AC: 2223 AN: 10592

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

European-Non Finnish (NFE) AF: 0.192 AC: 13084 AN: 67994

Other (OTH) AF: 0.165 AC: 350 AN: 2116

Alfa AF: 0.201 Hom.: 408

Bravo AF: 0.197

Asia WGS AF: 0.286 AC: 993 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	4.0
DANN	Benign	0.65
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs3920498; hg19: chr1-22492887;