18-43900562-C-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750746.1. 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
	ENSG00000297742	ENST00000750746.1		n.135+4357C>T		intron	N/A
	ENSG00000297742	ENST00000750747.1		n.129+4357C>T		intron	N/A
	ENSG00000297765	ENST00000750850.1		n.151+32672G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1380836;

hg19: chr18-41480527;