18-10394467-T-C

Variant names:

• chr18-10394467-T-C
• rs206530
• ENST00000754460.1:n.513+6499T>C

Variant summary

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

The ENST00000754460.1(ENSG00000287563):​n.513+6499T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,144 control chromosomes in the GnomAD database, including 36,857 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 0.69 (36857 hom., cov: 33)
• Consequence: ENSG00000287563 ENST00000754460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371989	XR_001753348.1	n.390-5603T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287563	ENST00000754460.1	n.513+6499T>C		intron_variant	Intron 3 of 3
ENSG00000287563	ENST00000754573.1	n.1038+6499T>C		intron_variant	Intron 2 of 3
ENSG00000287563	ENST00000754574.1	n.1050+6499T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105248 AN: 152026 Hom.: 36814 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.692 AC: 105356 AN: 152144 Hom.: 36857 Cov.: 33 AF XY: 0.689 AC XY: 51252 AN XY: 74380

African (AFR) AF: 0.789 AC: 32770 AN: 41538

American (AMR) AF: 0.661 AC: 10110 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2183 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3139 AN: 5146

South Asian (SAS) AF: 0.610 AC: 2941 AN: 4820

European-Finnish (FIN) AF: 0.666 AC: 7052 AN: 10586

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44800 AN: 67966

Other (OTH) AF: 0.686 AC: 1447 AN: 2110

Alfa AF: 0.669 Hom.: 4448

Bravo AF: 0.699

Asia WGS AF: 0.642 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.50
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs206530; hg19: chr18-10394464;