10-69194905-T-C

Variant names:

• chr10-69194905-T-C
• rs906217
• NM_003171.5:c.854-283T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003171.5(SUPV3L1):​c.854-283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,202 control chromosomes in the GnomAD database, including 57,667 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 0.87 (57667 hom., cov: 31)
• Consequence: SUPV3L1 NM_003171.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

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.854-283T>C		intron	N/A	NP_003162.2
	SUPV3L1	NM_001323585.2		c.491-283T>C		intron	N/A	NP_001310514.1
	SUPV3L1	NM_001323586.2		c.491-283T>C		intron	N/A	NP_001310515.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPV3L1	ENST00000359655.9	TSL:1 MANE Select	c.854-283T>C		intron	N/A	ENSP00000352678.4	Q8IYB8
	SUPV3L1	ENST00000956079.1		c.854-283T>C		intron	N/A	ENSP00000626138.1
	SUPV3L1	ENST00000917552.1		c.854-283T>C		intron	N/A	ENSP00000587611.1

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132073 AN: 152086 Hom.: 57636 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.868 AC: 132160 AN: 152202 Hom.: 57667 Cov.: 31 AF XY: 0.865 AC XY: 64367 AN XY: 74416

African (AFR) AF: 0.846 AC: 35125 AN: 41506

American (AMR) AF: 0.813 AC: 12436 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3237 AN: 3472

East Asian (EAS) AF: 0.640 AC: 3309 AN: 5170

South Asian (SAS) AF: 0.836 AC: 4031 AN: 4820

European-Finnish (FIN) AF: 0.887 AC: 9404 AN: 10604

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61624 AN: 68016

Other (OTH) AF: 0.883 AC: 1864 AN: 2112

Alfa AF: 0.885 Hom.: 7277

Bravo AF: 0.859

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.41
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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: rs906217; hg19: chr10-70954661;