ENST00000754460.1:n.513+6499T>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754460.1. 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	ENST00000754460.1		n.513+6499T>C		intron	N/A
	ENSG00000287563	ENST00000754573.1		n.1038+6499T>C		intron	N/A
	ENSG00000287563	ENST00000754574.1		n.1050+6499T>C		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs206530;

hg19: chr18-10394464;