rs17088536

Positions:

• chr8-22679714-G-A
• chr8-22679714-G-T

Variant summary

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

The ENST00000566457.1(ENSG00000261026):​n.4296C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 152,192 control chromosomes in the GnomAD database, including 207 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 0.047 (207 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: ENST00000566457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986924	XR_001745827.2	n.4324G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000566457.1	n.4296C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7061 AN: 152064 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0593

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0465 AC: 7077 AN: 152182 Hom.: 207 Cov.: 32 AF XY: 0.0486 AC XY: 3617 AN XY: 74406

Gnomad4 AFR AF: 0.0294

Gnomad4 AMR AF: 0.0405

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.0607

Gnomad4 NFE AF: 0.0445

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0447 Hom.: 19

Bravo AF: 0.0433

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
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: rs17088536; hg19: chr8-22537227;