ENST00000757451.1:n.251+3418G>A

Variant names:

• chr2-10435662-G-A
• rs2430419
• ENST00000757451.1:n.251+3418G>A

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.251+3418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,036 control chromosomes in the GnomAD database, including 9,103 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 0.32 (9103 hom., cov: 32)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 4 publications found

Genes affected

ENSG00000298698 (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 = 0.513 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
ENSG00000298698	ENST00000757451.1	n.251+3418G>A		intron_variant	Intron 1 of 1
ENSG00000298698	ENST00000757452.1	n.132+3418G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48695 AN: 151918 Hom.: 9085 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.321 AC: 48757 AN: 152036 Hom.: 9103 Cov.: 32 AF XY: 0.315 AC XY: 23399 AN XY: 74336

African (AFR) AF: 0.519 AC: 21499 AN: 41428

American (AMR) AF: 0.205 AC: 3134 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3472

East Asian (EAS) AF: 0.0871 AC: 450 AN: 5168

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4818

European-Finnish (FIN) AF: 0.268 AC: 2835 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17962 AN: 67956

Other (OTH) AF: 0.290 AC: 613 AN: 2114

Alfa AF: 0.179 Hom.: 429

Bravo AF: 0.321

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.86
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2430419; hg19: chr2-10575788;