1-234879452-C-T

Variant names:

• chr1-234879452-C-T
• rs2802955
• ENST00000651370.2:n.234+53017G>A

Variant summary

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

The ENST00000651370.2(ENSG00000286263):​n.234+53017G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,104 control chromosomes in the GnomAD database, including 48,469 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 0.79 (48469 hom., cov: 31)
• Consequence: ENSG00000286263 ENST00000651370.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 0 publications found

Genes affected

ENSG00000286263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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
ENSG00000286263	ENST00000651370.2	n.234+53017G>A		intron_variant	Intron 1 of 1
ENSG00000286263	ENST00000850398.1	n.309+33290G>A		intron_variant	Intron 2 of 2
ENSG00000286263	ENST00000850399.1	n.281+33290G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120232 AN: 151986 Hom.: 48405 Cov.: 31

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.791 AC: 120358 AN: 152104 Hom.: 48469 Cov.: 31 AF XY: 0.789 AC XY: 58668 AN XY: 74338

African (AFR) AF: 0.938 AC: 38951 AN: 41516

American (AMR) AF: 0.812 AC: 12405 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2491 AN: 3468

East Asian (EAS) AF: 0.945 AC: 4890 AN: 5172

South Asian (SAS) AF: 0.817 AC: 3940 AN: 4822

European-Finnish (FIN) AF: 0.628 AC: 6618 AN: 10540

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48493 AN: 67996

Other (OTH) AF: 0.773 AC: 1628 AN: 2106

Alfa AF: 0.736 Hom.: 64633

Bravo AF: 0.814

Asia WGS AF: 0.896 AC: 3114 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.19
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2802955; hg19: chr1-235015199; COSMIC: COSV70148404;