1-119494155-C-T

Variant names:

• chr1-119494155-C-T
• rs1856888
• ENST00000632456.2:n.243-4043G>A

Variant summary

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

The ENST00000632456.2(ENSG00000293080):​n.243-4043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,180 control chromosomes in the GnomAD database, including 34,769 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 (34769 hom., cov: 33)
• Consequence: ENSG00000293080 ENST00000632456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 8 publications found

Genes affected

ENSG00000293080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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
ENSG00000293080	ENST00000632456.2	n.243-4043G>A		intron_variant	Intron 2 of 6	6
ENSG00000293080	ENST00000756941.1	n.219-8547G>A		intron_variant	Intron 2 of 2
ENSG00000293080	ENST00000756942.1	n.259-4043G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102450 AN: 152062 Hom.: 34750 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.674 AC: 102519 AN: 152180 Hom.: 34769 Cov.: 33 AF XY: 0.683 AC XY: 50806 AN XY: 74388

African (AFR) AF: 0.637 AC: 26447 AN: 41504

American (AMR) AF: 0.736 AC: 11252 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2270 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4553 AN: 5172

South Asian (SAS) AF: 0.781 AC: 3769 AN: 4828

European-Finnish (FIN) AF: 0.737 AC: 7808 AN: 10598

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44108 AN: 67998

Other (OTH) AF: 0.660 AC: 1392 AN: 2110

Alfa AF: 0.576 Hom.: 1828

Bravo AF: 0.670

Asia WGS AF: 0.784 AC: 2727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.52
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1856888; hg19: chr1-120036778; COSMIC: COSV70872645;