ENST00000750746.1:n.135+4357C>T

Variant names:

• chr18-43900562-C-T
• rs1380836
• ENST00000750746.1:n.135+4357C>T

Variant summary

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

The ENST00000750746.1(ENSG00000297742):​n.135+4357C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,450 control chromosomes in the GnomAD database, including 33,072 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 0.66 (33072 hom., cov: 30)
• Consequence: ENSG00000297742 ENST00000750746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 6 publications found

Genes affected

ENSG00000297742 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372088	XR_935415.3	n.262+28511G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297742	ENST00000750746.1	n.135+4357C>T		intron_variant	Intron 1 of 6
ENSG00000297742	ENST00000750747.1	n.129+4357C>T		intron_variant	Intron 1 of 3
ENSG00000297765	ENST00000750850.1	n.151+32672G>A		intron_variant	Intron 1 of 1
ENSG00000297765	ENST00000750851.1	n.254+28511G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99669 AN: 151334 Hom.: 33027 Cov.: 30

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.659 AC: 99775 AN: 151450 Hom.: 33072 Cov.: 30 AF XY: 0.661 AC XY: 48907 AN XY: 73992

African (AFR) AF: 0.683 AC: 28244 AN: 41326

American (AMR) AF: 0.665 AC: 10096 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2312 AN: 3464

East Asian (EAS) AF: 0.841 AC: 4295 AN: 5104

South Asian (SAS) AF: 0.669 AC: 3222 AN: 4814

European-Finnish (FIN) AF: 0.635 AC: 6692 AN: 10542

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42672 AN: 67742

Other (OTH) AF: 0.643 AC: 1343 AN: 2088

Alfa AF: 0.640 Hom.: 135284

Bravo AF: 0.664

Asia WGS AF: 0.729 AC: 2533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.27
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs1380836; hg19: chr18-41480527;