rs594149

Variant names:

• chr1-182614182-C-G
• rs594149
• ENST00000718537.1:n.473-153C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-182614182-C-G
• chr1-182614182-C-T

Variant summary

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

The ENST00000718537.1(ENSG00000293719):​n.473-153C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,126 control chromosomes in the GnomAD database, including 54,221 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 0.84 (54221 hom., cov: 31)
• Consequence: ENSG00000293719 ENST00000718537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 2 publications found

Genes affected

ENSG00000293719 (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 = 0.952 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
ENSG00000293719	ENST00000718537.1	n.473-153C>G		intron_variant	Intron 2 of 2
ENSG00000293719	ENST00000718538.1	n.336-153C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127631 AN: 152008 Hom.: 54164 Cov.: 31

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.840 AC: 127744 AN: 152126 Hom.: 54221 Cov.: 31 AF XY: 0.834 AC XY: 61999 AN XY: 74344

African (AFR) AF: 0.960 AC: 39867 AN: 41516

American (AMR) AF: 0.794 AC: 12127 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2331 AN: 3472

East Asian (EAS) AF: 0.729 AC: 3770 AN: 5174

South Asian (SAS) AF: 0.814 AC: 3925 AN: 4822

European-Finnish (FIN) AF: 0.771 AC: 8142 AN: 10566

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54970 AN: 67986

Other (OTH) AF: 0.808 AC: 1703 AN: 2108

Alfa AF: 0.832 Hom.: 6561

Bravo AF: 0.843

Asia WGS AF: 0.809 AC: 2816 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	0.23
DANN	Benign	0.29
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs594149; hg19: chr1-182583317;