ENST00000757451.1:n.251+4062C>T

Variant names:

• chr2-10436306-C-T
• rs10929669
• ENST00000757451.1:n.251+4062C>T

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.251+4062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,246 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 34)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757451.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298698	ENST00000757451.1		n.251+4062C>T		intron	N/A
	ENSG00000298698	ENST00000757452.1		n.132+4062C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17042 AN: 152128 Hom.: 1053 Cov.: 34

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.112 AC: 17032 AN: 152246 Hom.: 1052 Cov.: 34 AF XY: 0.115 AC XY: 8524 AN XY: 74428

African (AFR) AF: 0.0731 AC: 3038 AN: 41556

American (AMR) AF: 0.0989 AC: 1513 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1366 AN: 5164

South Asian (SAS) AF: 0.119 AC: 572 AN: 4826

European-Finnish (FIN) AF: 0.181 AC: 1921 AN: 10600

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7767 AN: 68012

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.116 Hom.: 134

Bravo AF: 0.104

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.48
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs10929669; hg19: chr2-10576432;