rs607541

chr15-45642671-C-Achr15-45642671-C-Gchr15-45642671-C-T

Variant summary

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

The NM_021199.4(SQOR):c.-18+7563C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,984 control chromosomes in the GnomAD database, including 6,635 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 0.26 (6635 hom., cov: 32)
• Consequence: SQOR NM_021199.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.74

Genes affected

SQOR (HGNC:20390): (sulfide quinone oxidoreductase) The protein encoded by this gene may function in mitochondria to catalyze the conversion of sulfide to persulfides, thereby decreasing toxic concencrations of sulfide. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SQOR	NM_021199.4	c.-18+7563C>A		intron_variant		ENST00000260324.12
SQOR	NM_001271213.2	c.-18+10652C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SQOR	ENST00000260324.12	c.-18+7563C>A		intron_variant		1	NM_021199.4	P1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39874 AN: 151864 Hom.: 6606 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.263 AC: 39948 AN: 151984 Hom.: 6635 Cov.: 32 AF XY: 0.265 AC XY: 19697 AN XY: 74306

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.264

Alfa AF: 0.184 Hom.: 4847

Bravo AF: 0.292

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.0060
Dann	Benign	0.68

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: rs607541; hg19: chr15-45934869;