rs12412945

chr10-53038347-C-T

Variant summary

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

The ENST00000442866.1(SNRPEP8):n.63C>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 0.134 in 152,904 control chromosomes in the GnomAD database, including 1,610 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 0.13 (1596 hom., cov: 34)
  • Exomes 𝑓: 0.19 (14 hom.)
• Consequence: SNRPEP8 ENST00000442866.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

SNRPEP8 (HGNC:43573): (SNRPE pseudogene 8)

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 = 0.211 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
SNRPEP8	ENST00000442866.1	n.63C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20283 AN: 152130 Hom.: 1590 Cov.: 34

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.188 AC: 123 AN: 656 Hom.: 14 Cov.: 0 AF XY: 0.218 AC XY: 75 AN XY: 344

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.189

Gnomad4 NFE exome AF: 0.219

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.133 AC: 20296 AN: 152248 Hom.: 1596 Cov.: 34 AF XY: 0.133 AC XY: 9867 AN XY: 74440

Gnomad4 AFR AF: 0.0430

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.130

Alfa AF: 0.162 Hom.: 1005

Bravo AF: 0.129

Asia WGS AF: 0.179 AC: 622 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	2.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12412945; hg19: chr10-54798107;