chr2-42023409-C-T

Variant names:

• chr2-42023409-C-T
• rs7584262
• ENST00000451514.1:n.158-1156G>A

Variant summary

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

The ENST00000451514.1(ENSG00000226398):​n.158-1156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,980 control chromosomes in the GnomAD database, including 5,917 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 0.26 (5917 hom., cov: 32)
• Consequence: ENSG00000226398 ENST00000451514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 29 publications found

Genes affected

ENSG00000226398 (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 (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451514.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226398	ENST00000451514.1	TSL:5	n.158-1156G>A		intron	N/A
	ENSG00000226398	ENST00000777407.1		n.236+1737G>A		intron	N/A
	ENSG00000226398	ENST00000777408.1		n.217+1737G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40207 AN: 151862 Hom.: 5909 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.265 AC: 40248 AN: 151980 Hom.: 5917 Cov.: 32 AF XY: 0.264 AC XY: 19614 AN XY: 74264

African (AFR) AF: 0.375 AC: 15546 AN: 41424

American (AMR) AF: 0.182 AC: 2785 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5172

South Asian (SAS) AF: 0.224 AC: 1076 AN: 4808

European-Finnish (FIN) AF: 0.261 AC: 2751 AN: 10542

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15808 AN: 67978

Other (OTH) AF: 0.264 AC: 557 AN: 2108

Alfa AF: 0.240 Hom.: 12724

Bravo AF: 0.263

Asia WGS AF: 0.129 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.0
DANN	Benign	0.69
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs7584262; hg19: chr2-42250549;