15-45668699-C-T

Position:

• chr15-45668699-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.406-1229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 152,220 control chromosomes in the GnomAD database, including 518 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 0.078 (518 hom., cov: 32)
• Consequence: SQOR NM_021199.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SQOR	NM_021199.4	c.406-1229C>T		intron_variant		ENST00000260324.12
SQOR	NM_001271213.2	c.406-1229C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SQOR	ENST00000260324.12	c.406-1229C>T		intron_variant		1	NM_021199.4	P1

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11801 AN: 152102 Hom.: 518 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0776 AC: 11812 AN: 152220 Hom.: 518 Cov.: 32 AF XY: 0.0780 AC XY: 5810 AN XY: 74442

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0460

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0908

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0680 Hom.: 563

Bravo AF: 0.0734

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.51

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: rs11637483; hg19: chr15-45960897;