rs17060993

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000253899 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0258 AC: 11 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.122 AC: 5071 AN: 41556

American (AMR) AF: 0.0520 AC: 795 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4824

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10624

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0471 AC: 3204 AN: 68028

Other (OTH) AF: 0.0671 AC: 142 AN: 2116

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
PhyloP100		5.3

Splicing

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

Other links and lift over

dbSNP: rs17060993; hg19: chr8-26922112;