rs17066829

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000285681	ENST00000650201.1	n.113+33488T>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+33488T>A		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.367

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17066829; hg19: chr18-58030066;