rs480752

Variant names:

• chr1-181818649-C-A
• rs480752
• ENST00000717053.1:n.433-7706G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-181818649-C-A
• chr1-181818649-C-T

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.433-7706G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,994 control chromosomes in the GnomAD database, including 2,939 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 (2939 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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.433-7706G>T		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717054.1	n.438-7686G>T		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717055.1	n.226-7686G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28604 AN: 151876 Hom.: 2938 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.188 AC: 28608 AN: 151994 Hom.: 2939 Cov.: 32 AF XY: 0.188 AC XY: 13941 AN XY: 74298

African (AFR) AF: 0.255 AC: 10588 AN: 41462

American (AMR) AF: 0.142 AC: 2169 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3462

East Asian (EAS) AF: 0.0348 AC: 180 AN: 5174

South Asian (SAS) AF: 0.204 AC: 983 AN: 4816

European-Finnish (FIN) AF: 0.204 AC: 2155 AN: 10578

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11420 AN: 67908

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.170 Hom.: 4256

Bravo AF: 0.185

Asia WGS AF: 0.135 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.48
DANN	Benign	0.50
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs480752; hg19: chr1-181787784;