rs17154962

chr8-8933998-C-T

Variant summary

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

The ENST00000603391.1(ENSG00000270966):n.9G>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 0.11 in 1,581,632 control chromosomes in the GnomAD database, including 12,903 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 0.17 (3372 hom., cov: 32)
  • Exomes 𝑓: 0.10 (9531 hom.)
• Consequence: ENST00000603391.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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
	ENST00000603391.1	n.9G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26003 AN: 151958 Hom.: 3369 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.103 AC: 147575 AN: 1429556 Hom.: 9531 Cov.: 28 AF XY: 0.103 AC XY: 73418 AN XY: 712712

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.0664

Gnomad4 ASJ exome AF: 0.0721

Gnomad4 EAS exome AF: 0.144

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.131

Gnomad4 NFE exome AF: 0.0921

Gnomad4 OTH exome AF: 0.119

GnomAD4 genome AF: 0.171 AC: 26036 AN: 152076 Hom.: 3372 Cov.: 32 AF XY: 0.173 AC XY: 12858 AN XY: 74360

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.0965

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0923

Gnomad4 OTH AF: 0.152

Alfa AF: 0.132 Hom.: 341

Bravo AF: 0.178

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17154962; hg19: chr8-8791508;