rs10998624

Variant names:

• chr10-69180045-G-A
• rs10998624
• NM_003171.5:c.-247G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-69180045-G-A
• chr10-69180045-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 12 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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.-247G>A		upstream_gene	N/A	NP_003162.2
	SUPV3L1	NM_001323585.2		c.-818G>A		upstream_gene	N/A	NP_001310514.1
	SUPV3L1	NM_001323586.2		c.-683G>A		upstream_gene	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.-247G>A		upstream_gene	N/A	ENSP00000352678.4	Q8IYB8
	SUPV3L1	ENST00000471069.5	TSL:1	n.-205G>A		upstream_gene	N/A
	SUPV3L1	ENST00000956079.1		c.-247G>A		upstream_gene	N/A	ENSP00000626138.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16730 AN: 152112 Hom.: 2281 Cov.: 32

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.: 32 AF XY: 0.108 AC XY: 8010 AN XY: 74442

African (AFR) AF: 0.324 AC: 13464 AN: 41496

American (AMR) AF: 0.0608 AC: 930 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0547 AC: 190 AN: 3472

East Asian (EAS) AF: 0.104 AC: 539 AN: 5186

South Asian (SAS) AF: 0.0726 AC: 351 AN: 4832

European-Finnish (FIN) AF: 0.00594 AC: 63 AN: 10612

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1026 AN: 68026

Other (OTH) AF: 0.0913 AC: 193 AN: 2114

Alfa AF: 0.0418 Hom.: 2612

Bravo AF: 0.123

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.8
DANN	Benign	0.90
PhyloP100		-0.29
PromoterAI		0.094	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10998624; hg19: chr10-70939801;