10-13328315-C-T

Variant names:

• chr10-13328315-C-T
• rs3740211
• NM_012247.5:c.751+36G>A

Variant summary

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

The NM_012247.5(SEPHS1):​c.751+36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,380,884 control chromosomes in the GnomAD database, including 190,224 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 0.45 (17097 hom., cov: 31)
  • Exomes 𝑓: 0.52 (173127 hom.)
• Consequence: SEPHS1 NM_012247.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

Genes affected

SEPHS1 (HGNC:19685): (selenophosphate synthetase 1) This gene encodes an enzyme that synthesizes selenophosphate from selenide and ATP. Selenophosphate is the selenium donor used to synthesize selenocysteine, which is co-translationally incorporated into selenoproteins at in-frame UGA codons. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPHS1	NM_012247.5	c.751+36G>A		intron_variant	Intron 7 of 8	ENST00000327347.10	NP_036379.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEPHS1	ENST00000327347.10	c.751+36G>A		intron_variant	Intron 7 of 8	1	NM_012247.5	ENSP00000367893.3
SEPHS1	ENST00000545675.5	c.550+36G>A		intron_variant	Intron 6 of 7	1		ENSP00000441119.2
SEPHS1	ENST00000378614.8	c.751+36G>A		intron_variant	Intron 7 of 7	1		ENSP00000367877.3

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67826 AN: 151758 Hom.: 17099 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.488

GnomAD3 exomes AF: 0.544 AC: 132352 AN: 243390 Hom.: 38302 AF XY: 0.545 AC XY: 71665 AN XY: 131488

Gnomad AFR exome AF: 0.201

Gnomad AMR exome AF: 0.703

Gnomad ASJ exome AF: 0.460

Gnomad EAS exome AF: 0.797

Gnomad SAS exome AF: 0.590

Gnomad FIN exome AF: 0.517

Gnomad NFE exome AF: 0.508

Gnomad OTH exome AF: 0.519

GnomAD4 exome AF: 0.524 AC: 643554 AN: 1229008 Hom.: 173127 Cov.: 16 AF XY: 0.526 AC XY: 327720 AN XY: 622984

Gnomad4 AFR exome AF: 0.189

Gnomad4 AMR exome AF: 0.695

Gnomad4 ASJ exome AF: 0.460

Gnomad4 EAS exome AF: 0.756

Gnomad4 SAS exome AF: 0.596

Gnomad4 FIN exome AF: 0.520

Gnomad4 NFE exome AF: 0.513

Gnomad4 OTH exome AF: 0.518

GnomAD4 genome AF: 0.447 AC: 67840 AN: 151876 Hom.: 17097 Cov.: 31 AF XY: 0.453 AC XY: 33614 AN XY: 74212

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.484

Alfa AF: 0.465 Hom.: 3588

Bravo AF: 0.443

Asia WGS AF: 0.619 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.52
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3740211; hg19: chr10-13370315;