rs17058952

Positions:

• chr8-28316837-A-G

Variant summary

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

The ENST00000521731.1(ENSG00000253690):​n.230+22189T>C 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 0.401 in 152,112 control chromosomes in the GnomAD database, including 12,676 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 0.40 (12671 hom., cov: 32)
  • Exomes 𝑓: 0.35 (5 hom.)
• Consequence: ENST00000521731.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 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
	ENST00000521731.1	n.230+22189T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60934 AN: 151932 Hom.: 12650 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.355 AC: 22 AN: 62 Hom.: 5 AF XY: 0.348 AC XY: 16 AN XY: 46

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.370

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.401 AC: 60991 AN: 152050 Hom.: 12671 Cov.: 32 AF XY: 0.404 AC XY: 30009 AN XY: 74330

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.410

Alfa AF: 0.368 Hom.: 8646

Bravo AF: 0.411

Asia WGS AF: 0.510 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17058952; hg19: chr8-28174354;