18-10382886-C-T

Variant names:

• chr18-10382886-C-T
• rs206548
• ENST00000653772.1:n.1141+1323C>T

Variant summary

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

The ENST00000653772.1(ENSG00000287563):​n.1141+1323C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,028 control chromosomes in the GnomAD database, including 16,137 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 0.44 (16137 hom., cov: 33)
• Consequence: ENSG00000287563 ENST00000653772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 1 publications found

Genes affected

ENSG00000287563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653772.1. 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
	ENSG00000287563	ENST00000653772.1		n.1141+1323C>T		intron	N/A
	ENSG00000287563	ENST00000754460.1		n.159-1225C>T		intron	N/A
	ENSG00000287563	ENST00000754573.1		n.911+1533C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67071 AN: 151910 Hom.: 16126 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.441 AC: 67114 AN: 152028 Hom.: 16137 Cov.: 33 AF XY: 0.445 AC XY: 33074 AN XY: 74328

African (AFR) AF: 0.246 AC: 10186 AN: 41466

American (AMR) AF: 0.505 AC: 7714 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2108 AN: 3462

East Asian (EAS) AF: 0.585 AC: 3027 AN: 5172

South Asian (SAS) AF: 0.642 AC: 3094 AN: 4818

European-Finnish (FIN) AF: 0.457 AC: 4823 AN: 10558

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.508 AC: 34521 AN: 67964

Other (OTH) AF: 0.464 AC: 981 AN: 2112

Alfa AF: 0.491 Hom.: 23313

Bravo AF: 0.436

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.63

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: rs206548;

hg19: chr18-10382883;