10-69180307-GCC-ACT

Variant names:

• chr10-69180307-GCC-ACT
• NM_003171.5:c.16_18delGCCinsACT
• SUPV3L1 p.Ala6Thr

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003171.5(SUPV3L1):​c.16_18delGCCinsACT​(p.Ala6Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A6S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SUPV3L1 NM_003171.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 0 publications found

Genes affected

SUPV3L1 (HGNC:11471): (Suv3 like RNA helicase) Enables helicase activity; nucleic acid binding activity; and protein homodimerization activity. Involved in several processes, including mitochondrial RNA metabolic process; mitochondrion morphogenesis; and positive regulation of mitochondrial RNA catabolic process. Located in mitochondrial nucleoid and nucleus. Part of mitochondrial degradosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003171.5. 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
	SUPV3L1	NM_003171.5	MANE Select	c.16_18delGCCinsACT	p.Ala6Thr	missense	N/A	NP_003162.2
	SUPV3L1	NM_001323585.2		c.-556_-554delGCCinsACT		5_prime_UTR	Exon 1 of 17	NP_001310514.1
	SUPV3L1	NM_001323586.2		c.-421_-419delGCCinsACT		5_prime_UTR	Exon 1 of 16	NP_001310515.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPV3L1	ENST00000359655.9	TSL:1 MANE Select	c.16_18delGCCinsACT	p.Ala6Thr	missense	N/A	ENSP00000352678.4	Q8IYB8
	SUPV3L1	ENST00000471069.5	TSL:1	n.58_60delGCCinsACT		non_coding_transcript_exon	Exon 1 of 6
	SUPV3L1	ENST00000956079.1		c.16_18delGCCinsACT	p.Ala6Thr	missense	N/A	ENSP00000626138.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr10-70940063;