rs9989529

Variant names:

• chr18-63114144-T-C
• rs9989529
• ENST00000763645.1:n.516-13875T>C

Variant summary

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

The ENST00000763645.1(ENSG00000299452):​n.516-13875T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,044 control chromosomes in the GnomAD database, including 12,027 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 0.38 (12027 hom., cov: 32)
• Consequence: ENSG00000299452 ENST00000763645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 6 publications found

Genes affected

ENSG00000299452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299452	ENST00000763645.1	n.516-13875T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57651 AN: 151928 Hom.: 12024 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.379 AC: 57672 AN: 152044 Hom.: 12027 Cov.: 32 AF XY: 0.378 AC XY: 28087 AN XY: 74336

African (AFR) AF: 0.223 AC: 9274 AN: 41496

American (AMR) AF: 0.310 AC: 4738 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3464

East Asian (EAS) AF: 0.167 AC: 865 AN: 5178

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4818

European-Finnish (FIN) AF: 0.539 AC: 5689 AN: 10554

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32900 AN: 67940

Other (OTH) AF: 0.379 AC: 800 AN: 2112

Alfa AF: 0.438 Hom.: 26841

Bravo AF: 0.352

Asia WGS AF: 0.238 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.62
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9989529; hg19: chr18-60781377;