rs28620398

Variant names:

• chr10-133659662-T-G
• rs28620398
• ENST00000438421.1:n.321+44A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000438421.1(CLUHP5):​n.321+44A>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLUHP5	ENST00000438421.1	n.321+44A>C		intron_variant	Intron 3 of 7	6

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5390 AN: 151940 Hom.: 1 Cov.: 42

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

African (AFR) AF: 0.127 AC: 1157 AN: 9116

American (AMR) AF: 0.00678 AC: 196 AN: 28890

Ashkenazi Jewish (ASJ) AF: 0.0000944 AC: 1 AN: 10588

East Asian (EAS) AF: 0.00 AC: 0 AN: 10218

South Asian (SAS) AF: 0.000217 AC: 13 AN: 60040

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26178

Middle Eastern (MID) AF: 0.00480 AC: 12 AN: 2498

European-Non Finnish (NFE) AF: 0.000590 AC: 95 AN: 160968

Other (OTH) AF: 0.00825 AC: 119 AN: 14424

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.123 AC: 5095 AN: 41316

American (AMR) AF: 0.0139 AC: 213 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5158

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10632

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000603 AC: 41 AN: 68028

Other (OTH) AF: 0.0265 AC: 56 AN: 2114

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs28620398; hg19: chr10-135473166;