chr1-181852272-C-T

Variant names:

• chr1-181852272-C-T
• rs4465155
• ENST00000717053.1:n.288-16636G>A

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-16636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,636 control chromosomes in the GnomAD database, including 5,716 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 0.25 (5716 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 1 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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
ENSG00000287452	ENST00000717053.1	n.288-16636G>A		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1	n.293-16636G>A		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717055.1	n.81-16636G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38235 AN: 151518 Hom.: 5706 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.252 AC: 38259 AN: 151636 Hom.: 5716 Cov.: 32 AF XY: 0.253 AC XY: 18760 AN XY: 74070

African (AFR) AF: 0.0836 AC: 3457 AN: 41370

American (AMR) AF: 0.304 AC: 4631 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3464

East Asian (EAS) AF: 0.388 AC: 1985 AN: 5118

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4812

European-Finnish (FIN) AF: 0.266 AC: 2778 AN: 10448

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.322 AC: 21885 AN: 67882

Other (OTH) AF: 0.260 AC: 548 AN: 2110

Alfa AF: 0.253 Hom.: 4140

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.43
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs4465155; hg19: chr1-181821407;