10-69194905-T-C

Position:

• chr10-69194905-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000359655.9(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 ENST00000359655.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUPV3L1	NM_003171.5	c.854-283T>C		intron_variant		ENST00000359655.9	NP_003162.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUPV3L1	ENST00000359655.9	c.854-283T>C		intron_variant		1	NM_003171.5	ENSP00000352678	P1

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

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.883

Alfa AF: 0.888 Hom.: 7010

Bravo AF: 0.859

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs906217; hg19: chr10-70954661;