rs17066866

chr18-60388386-A-T

Variant summary

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

The ENST00000658928.1(ENSG00000285681):n.156+59041A>T 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 0.0665 in 152,104 control chromosomes in the GnomAD database, including 833 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 0.066 (833 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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+59041A>T		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+59041A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10072 AN: 151986 Hom.: 824 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0214

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.00405

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0665 AC: 10110 AN: 152104 Hom.: 833 Cov.: 32 AF XY: 0.0637 AC XY: 4733 AN XY: 74338

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0313

Gnomad4 ASJ AF: 0.0214

Gnomad4 EAS AF: 0.0219

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.00405

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0465 Hom.: 58

Bravo AF: 0.0738

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17066866; hg19: chr18-58055619;