rs28620398

chr10-133659662-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000438421.1(CLUHP5):n.321+44A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.036 (1 hom., cov: 42)
  • Exomes 𝑓: 0.0049 (16 hom.)
  • Failed GnomAD Quality Control
• Consequence: CLUHP5 ENST00000438421.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

Genes affected

CLUHP5 (HGNC:38471): (clustered mitochondria homolog pseudogene 5)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLUHP5	ENST00000438421.1	n.321+44A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 5390 AN: 151940 Hom.: 1 Cov.: 42 FAILED QC

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000603

Gnomad OTH AF: 0.0268

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00493 AC: 1593 AN: 322920 Hom.: 16 Cov.: 0 AF XY: 0.00358 AC XY: 653 AN XY: 182500

Gnomad4 AFR exome AF: 0.127

Gnomad4 AMR exome AF: 0.00678

Gnomad4 ASJ exome AF: 0.0000944

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000217

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000590

Gnomad4 OTH exome AF: 0.00825

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0356 AC: 5408 AN: 152058 Hom.: 1 Cov.: 42 AF XY: 0.0349 AC XY: 2592 AN XY: 74358

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000603

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0311 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.1
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28620398; hg19: chr10-135473166;