rs17066829

chr18-60362833-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658928.1(ENSG00000285681):n.156+33488T>A variant causes a intron, non coding transcript 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: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658928.1	n.156+33488T>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+33488T>A		intron_variant, non_coding_transcript_variant

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;