rs17066829

Variant names:

• chr18-60362833-T-A
• rs17066829
• ENST00000650201.1:n.113+33488T>A

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+33488T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,038 control chromosomes in the GnomAD database, including 11,918 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 (11918 hom., cov: 33)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 12 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650201.1. 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
	ENSG00000285681	ENST00000650201.1		n.113+33488T>A		intron	N/A
	ENSG00000285681	ENST00000658928.1		n.156+33488T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58130 AN: 151920 Hom.: 11896 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.383 AC: 58189 AN: 152038 Hom.: 11918 Cov.: 33 AF XY: 0.374 AC XY: 27832 AN XY: 74324

African (AFR) AF: 0.528 AC: 21885 AN: 41486

American (AMR) AF: 0.383 AC: 5842 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1092 AN: 5176

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4824

European-Finnish (FIN) AF: 0.247 AC: 2618 AN: 10582

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22858 AN: 67920

Other (OTH) AF: 0.367 AC: 775 AN: 2112

Alfa AF: 0.357 Hom.: 1452

Bravo AF: 0.404

Asia WGS AF: 0.275 AC: 957 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17066829; hg19: chr18-58030066;