ENST00000725701.1:n.411+29869C>T

Variant names:

• chr1-22218804-C-T
• rs10917176
• ENST00000725701.1:n.411+29869C>T

Variant summary

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

The ENST00000725701.1(ENSG00000294752):​n.411+29869C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,018 control chromosomes in the GnomAD database, including 3,506 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 (3506 hom., cov: 31)
• Consequence: ENSG00000294752 ENST00000725701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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
ENSG00000294752	ENST00000725701.1	n.411+29869C>T		intron_variant	Intron 3 of 3
ENSG00000294752	ENST00000725702.1	n.235+29869C>T		intron_variant	Intron 2 of 2
ENSG00000294752	ENST00000725703.1	n.219-11102C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30067 AN: 151900 Hom.: 3503 Cov.: 31

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.198 AC: 30078 AN: 152018 Hom.: 3506 Cov.: 31 AF XY: 0.203 AC XY: 15071 AN XY: 74276

African (AFR) AF: 0.0969 AC: 4017 AN: 41474

American (AMR) AF: 0.273 AC: 4171 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2466 AN: 5130

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2372 AN: 10550

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14648 AN: 67974

Other (OTH) AF: 0.203 AC: 428 AN: 2108

Alfa AF: 0.198 Hom.: 438

Bravo AF: 0.200

Asia WGS AF: 0.319 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.051
DANN	Benign	0.54
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10917176; hg19: chr1-22545297;