rs360234

Variant names:

• chr2-126283978-C-T
• rs360234
• ENST00000703015.1:n.356+24022G>A

Variant summary

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

The ENST00000703015.1(ENSG00000290113):​n.356+24022G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 151,960 control chromosomes in the GnomAD database, including 47,027 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 0.78 (47027 hom., cov: 30)
• Consequence: ENSG00000290113 ENST00000703015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 7 publications found

Genes affected

ENSG00000290113 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 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
ENSG00000290113	ENST00000703015.1	n.356+24022G>A		intron_variant	Intron 1 of 1
ENSG00000290113	ENST00000797885.1	n.335+24022G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117749 AN: 151844 Hom.: 46983 Cov.: 30

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.775 AC: 117845 AN: 151960 Hom.: 47027 Cov.: 30 AF XY: 0.768 AC XY: 57059 AN XY: 74264

African (AFR) AF: 0.947 AC: 39323 AN: 41524

American (AMR) AF: 0.648 AC: 9889 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2428 AN: 3438

East Asian (EAS) AF: 0.446 AC: 2289 AN: 5138

South Asian (SAS) AF: 0.541 AC: 2601 AN: 4804

European-Finnish (FIN) AF: 0.761 AC: 8016 AN: 10534

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50887 AN: 67956

Other (OTH) AF: 0.751 AC: 1584 AN: 2110

Alfa AF: 0.749 Hom.: 63979

Bravo AF: 0.773

Asia WGS AF: 0.502 AC: 1745 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.40
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs360234; hg19: chr2-127041555;