dbSNP rs10998624: SUPV3L1:c.-247G>A (chr10-69180045-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003171.5(SUPV3L1):c.-247G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,230 control chromosomes in the GnomAD database, including 2,296 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 0.11 ( 2296 hom., cov: 32)

Consequence

SUPV3L1
NM_003171.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291

Variant links:

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]

SUPV3L1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPV3L1	NM_003171.5 link	c.-247G>A		upstream_gene_variant		ENST00000359655.9	NP_003162.2	Q8IYB8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SUPV3L1	ENST00000359655.9 link	c.-247G>A	upstream_gene_variant	1	NM_003171.5	ENSP00000352678.4	Q8IYB8
SUPV3L1	ENST00000471069.5 link	n.-205G>A	upstream_gene_variant	1
SUPV3L1	ENST00000422378.1 link	c.-247G>A	upstream_gene_variant	5		ENSP00000409072.1	B1AR60
SUPV3L1	ENST00000483572.5 link	n.-236G>A	upstream_gene_variant	5

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16730

AN:

152112

Hom.:

2281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.0231

Gnomad AMR

AF:

0.0609

Gnomad ASJ

AF:

0.0547

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.0730

Gnomad FIN

AF:

0.00594

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0151

Gnomad OTH

AF:

0.0908

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

GnomAD4 genome

AF:

0.110

AC:

16786

AN:

152230

Hom.:

2296

Cov.:

AF XY:

0.108

AC XY:

8010

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.0608

Gnomad4 ASJ

AF:

0.0547

Gnomad4 EAS

AF:

0.104

Gnomad4 SAS

AF:

0.0726

Gnomad4 FIN

AF:

0.00594

Gnomad4 NFE

AF:

0.0151

Gnomad4 OTH

AF:

0.0913

Alfa

AF:

0.0259

Hom.:

431

Bravo

AF:

0.123

Asia WGS

AF:

0.111

AC:

385

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.8

DANN

Benign

0.90

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over