rs17470994

Positions:

• chr15-49012128-G-C

Variant summary

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

The NM_001193489.2(SECISBP2L):​c.1732-265C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 110,076 control chromosomes in the GnomAD database, including 229 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 0.062 (229 hom., cov: 32)
• Consequence: SECISBP2L NM_001193489.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

SECISBP2L (HGNC:28997): (SECIS binding protein 2 like) Enables RNA binding activity. Predicted to be involved in selenocysteine incorporation. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SECISBP2L	NM_001193489.2	c.1732-265C>G		intron_variant		ENST00000559471.6
SECISBP2L	NM_014701.4	c.1597-265C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SECISBP2L	ENST00000559471.6	c.1732-265C>G		intron_variant		1	NM_001193489.2	P4
SECISBP2L	ENST00000261847.7	c.1597-265C>G		intron_variant		1		A1
SECISBP2L	ENST00000380927.6	c.1018-265C>G		intron_variant		1
SECISBP2L	ENST00000559198.1	n.495-265C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0622 AC: 6844 AN: 109964 Hom.: 228 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.000429

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0621 AC: 6837 AN: 110076 Hom.: 229 Cov.: 32 AF XY: 0.0599 AC XY: 3211 AN XY: 53650

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.000430

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.0345

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0462 Hom.: 20

Bravo AF: 0.0467

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.89
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: rs17470994; hg19: chr15-49304325;