18-10520293-T-A

Variant names:

• chr18-10520293-T-A
• rs473938
• ENST00000763663.1:n.575T>A

Variant summary

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

The ENST00000763663.1(ENSG00000299454):​n.575T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,038 control chromosomes in the GnomAD database, including 25,786 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 0.56 (25786 hom., cov: 32)
• Consequence: ENSG00000299454 ENST00000763663.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 3 publications found

Genes affected

ENSG00000299454 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763663.1. 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
	ENSG00000299454	ENST00000763663.1		n.575T>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299454	ENST00000763664.1		n.353T>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84738 AN: 151920 Hom.: 25751 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.558 AC: 84827 AN: 152038 Hom.: 25786 Cov.: 32 AF XY: 0.554 AC XY: 41128 AN XY: 74296

African (AFR) AF: 0.809 AC: 33587 AN: 41494

American (AMR) AF: 0.491 AC: 7505 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3472

East Asian (EAS) AF: 0.690 AC: 3558 AN: 5156

South Asian (SAS) AF: 0.432 AC: 2079 AN: 4808

European-Finnish (FIN) AF: 0.435 AC: 4589 AN: 10550

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30252 AN: 67954

Other (OTH) AF: 0.507 AC: 1072 AN: 2116

Alfa AF: 0.509 Hom.: 2611

Bravo AF: 0.579

Asia WGS AF: 0.519 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.52
PhyloP100		-2.2

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: rs473938;

hg19: chr18-10520290;