rs486003

Variant names:

• chr1-181844634-A-G
• rs486003
• ENST00000717053.1:n.288-8998T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-181844634-A-G
• chr1-181844634-A-T

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-8998T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,008 control chromosomes in the GnomAD database, including 34,967 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 0.68 (34967 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717053.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287452	ENST00000717053.1		n.288-8998T>C		intron	N/A
	ENSG00000287452	ENST00000717054.1		n.293-8998T>C		intron	N/A
	ENSG00000287452	ENST00000717055.1		n.81-8998T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102656 AN: 151890 Hom.: 34938 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.676 AC: 102736 AN: 152008 Hom.: 34967 Cov.: 32 AF XY: 0.675 AC XY: 50152 AN XY: 74290

African (AFR) AF: 0.603 AC: 24989 AN: 41452

American (AMR) AF: 0.671 AC: 10261 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2441 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2963 AN: 5154

South Asian (SAS) AF: 0.778 AC: 3747 AN: 4818

European-Finnish (FIN) AF: 0.673 AC: 7104 AN: 10552

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48946 AN: 67966

Other (OTH) AF: 0.695 AC: 1465 AN: 2108

Alfa AF: 0.706 Hom.: 120639

Bravo AF: 0.669

Asia WGS AF: 0.673 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.76
PhyloP100		-0.81

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs486003;

hg19: chr1-181813769;