rs281366

Positions:

• chr17-19897081-C-T

Variant summary

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

The ENST00000602353.1(ENSG00000270091):​n.190G>A 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 0.04 in 152,198 control chromosomes in the GnomAD database, including 176 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 0.040 (176 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000602353.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0823 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
	ENST00000602353.1	n.190G>A		non_coding_transcript_exon_variant	1/1
	ENST00000602532.1	n.207G>A		non_coding_transcript_exon_variant	1/2	5

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6076 AN: 152080 Hom.: 176 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0292

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0400 AC: 6082 AN: 152198 Hom.: 176 Cov.: 32 AF XY: 0.0377 AC XY: 2806 AN XY: 74412

Gnomad4 AFR AF: 0.0846

Gnomad4 AMR AF: 0.0241

Gnomad4 ASJ AF: 0.00923

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0192

Gnomad4 NFE AF: 0.0250

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0379 Hom.: 49

Bravo AF: 0.0418

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281366; hg19: chr17-19800394;