2-224183027-T-C

Variant names:

• chr2-224183027-T-C
• rs2629046
• ENST00000745604.1:n.129+27302A>G

Variant summary

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

The ENST00000745604.1(ENSG00000297115):​n.129+27302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,072 control chromosomes in the GnomAD database, including 21,731 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 0.52 (21731 hom., cov: 32)
• Consequence: ENSG00000297115 ENST00000745604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 31 publications found

Genes affected

ENSG00000297115 (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 (AFR) allele frequency at 95% confidence interval = 0.677 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
ENSG00000297115	ENST00000745604.1	n.129+27302A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79599 AN: 151954 Hom.: 21710 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.524 AC: 79671 AN: 152072 Hom.: 21731 Cov.: 32 AF XY: 0.522 AC XY: 38785 AN XY: 74330

African (AFR) AF: 0.684 AC: 28370 AN: 41496

American (AMR) AF: 0.476 AC: 7263 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1525 AN: 3466

East Asian (EAS) AF: 0.624 AC: 3224 AN: 5166

South Asian (SAS) AF: 0.450 AC: 2169 AN: 4820

European-Finnish (FIN) AF: 0.462 AC: 4882 AN: 10566

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30632 AN: 67966

Other (OTH) AF: 0.495 AC: 1047 AN: 2114

Alfa AF: 0.474 Hom.: 67764

Bravo AF: 0.533

Asia WGS AF: 0.538 AC: 1869 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.58
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2629046; hg19: chr2-225047744;