17-2695345-C-T

Variant names:

• chr17-2695345-C-T
• rs1003399
• NM_001366661.1:c.2544+29G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001366661.1(CLUH):​c.2544+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
• Consequence: CLUH NM_001366661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 15 publications found

Genes affected

CLUH (HGNC:29094): (clustered mitochondria homolog) Enables mRNA binding activity. Involved in intracellular distribution of mitochondria. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366661.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLUH	NM_001366661.1	MANE Select	c.2544+29G>A		intron	N/A	NP_001353590.1	A0A494C0R8
	CLUH	NM_015229.4		c.2541+29G>A		intron	N/A	NP_056044.4
	CLUH	NM_001366662.1		c.2427+29G>A		intron	N/A	NP_001353591.1	O75153

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLUH	ENST00000651024.2	MANE Select	c.2544+29G>A		intron	N/A	ENSP00000498679.1	A0A494C0R8
	CLUH	ENST00000876318.1		c.2562+29G>A		intron	N/A	ENSP00000546377.1
	CLUH	ENST00000876317.1		c.2559+29G>A		intron	N/A	ENSP00000546376.1

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Cov.: 66

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.22
DANN	Benign	0.74
PhyloP100		-1.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1003399; hg19: chr17-2598639;