rs17060993

Variant names:

• chr8-27064595-T-A
• rs17060993
• ENST00000517322.1:n.684A>T

Variant summary

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

The ENST00000517322.1(ENSG00000253899):​n.684A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0644 in 152,752 control chromosomes in the GnomAD database, including 471 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 0.065 (471 hom., cov: 33)
  • Exomes 𝑓: 0.025 (0 hom.)
• Consequence: ENSG00000253899 ENST00000517322.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.28

Genes affected

ENSG00000253899 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 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
ENSG00000253899	ENST00000517322.1	n.684A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9815 AN: 152202 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0521

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0471

Gnomad OTH AF: 0.0678

GnomAD4 exome AF: 0.0255 AC: 11 AN: 432 Hom.: 0 Cov.: 0 AF XY: 0.0308 AC XY: 8 AN XY: 260

Gnomad4 FIN exome AF: 0.0258

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0645 AC: 9830 AN: 152320 Hom.: 471 Cov.: 33 AF XY: 0.0614 AC XY: 4572 AN XY: 74486

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0520

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0471

Gnomad4 OTH AF: 0.0671

Alfa AF: 0.0557 Hom.: 32

Bravo AF: 0.0724

Asia WGS AF: 0.0140 AC: 49 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17060993; hg19: chr8-26922112;