1-181841058-T-C

Variant names:

• chr1-181841058-T-C
• rs585315
• ENST00000717053.1:n.288-5422A>G

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-5422A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,942 control chromosomes in the GnomAD database, including 34,440 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 0.67 (34440 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 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.288-5422A>G		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1	n.293-5422A>G		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717055.1	n.81-5422A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101844 AN: 151824 Hom.: 34409 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.671 AC: 101926 AN: 151942 Hom.: 34440 Cov.: 32 AF XY: 0.670 AC XY: 49747 AN XY: 74254

African (AFR) AF: 0.596 AC: 24702 AN: 41428

American (AMR) AF: 0.664 AC: 10126 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2428 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2981 AN: 5176

South Asian (SAS) AF: 0.775 AC: 3738 AN: 4822

European-Finnish (FIN) AF: 0.673 AC: 7092 AN: 10544

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.715 AC: 48599 AN: 67942

Other (OTH) AF: 0.686 AC: 1446 AN: 2108

Alfa AF: 0.688 Hom.: 7068

Bravo AF: 0.663

Asia WGS AF: 0.670 AC: 2327 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.62
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs585315; hg19: chr1-181810193;