chr18-78675166-G-A

Variant names:

• chr18-78675166-G-A
• rs12605652
• ENST00000759065.1:n.186-3316C>T

Variant summary

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

The ENST00000759065.1(ENSG00000298930):​n.186-3316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 150,192 control chromosomes in the GnomAD database, including 10,017 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 0.33 (10017 hom., cov: 29)
• Consequence: ENSG00000298930 ENST00000759065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 1 publications found

Genes affected

ENSG00000298930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 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
ENSG00000298930	ENST00000759065.1	n.186-3316C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.331 AC: 49735 AN: 150080 Hom.: 10014 Cov.: 29

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.331 AC: 49731 AN: 150192 Hom.: 10017 Cov.: 29 AF XY: 0.340 AC XY: 24897 AN XY: 73236

African (AFR) AF: 0.0898 AC: 3642 AN: 40562

American (AMR) AF: 0.390 AC: 5901 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3466

East Asian (EAS) AF: 0.643 AC: 3273 AN: 5090

South Asian (SAS) AF: 0.474 AC: 2236 AN: 4714

European-Finnish (FIN) AF: 0.496 AC: 5077 AN: 10246

Middle Eastern (MID) AF: 0.366 AC: 106 AN: 290

European-Non Finnish (NFE) AF: 0.403 AC: 27295 AN: 67698

Other (OTH) AF: 0.356 AC: 743 AN: 2088

Alfa AF: 0.373 Hom.: 18266

Bravo AF: 0.310

Asia WGS AF: 0.541 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.46
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs12605652; hg19: chr18-76435166;