ENST00000733295.1:n.262-360T>C

Variant names:

• chr10-124381580-A-G
• rs12218361
• ENST00000733295.1:n.262-360T>C

Variant summary

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

The ENST00000733295.1(ENSG00000295867):​n.262-360T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,070 control chromosomes in the GnomAD database, including 2,018 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 0.13 (2018 hom., cov: 32)
• Consequence: ENSG00000295867 ENST00000733295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 2 publications found

Genes affected

ENSG00000295867 (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 = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733295.1. 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
	ENSG00000295867	ENST00000733295.1		n.262-360T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19162 AN: 151952 Hom.: 2010 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.126 AC: 19201 AN: 152070 Hom.: 2018 Cov.: 32 AF XY: 0.126 AC XY: 9362 AN XY: 74364

African (AFR) AF: 0.268 AC: 11064 AN: 41334

American (AMR) AF: 0.0813 AC: 1244 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.187 AC: 968 AN: 5172

South Asian (SAS) AF: 0.123 AC: 592 AN: 4828

European-Finnish (FIN) AF: 0.0309 AC: 328 AN: 10628

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0631 AC: 4292 AN: 68024

Other (OTH) AF: 0.129 AC: 272 AN: 2110

Alfa AF: 0.0615 Hom.: 121

Bravo AF: 0.137

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.30
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs12218361; hg19: chr10-126070149;