chr15-49036706-C-G

Variant names:

• chr15-49036706-C-G
• rs877007
• NM_001193489.2:c.203+885G>C

Variant summary

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

The NM_001193489.2(SECISBP2L):​c.203+885G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,130 control chromosomes in the GnomAD database, including 22,311 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 0.52 (22311 hom., cov: 33)
• Consequence: SECISBP2L NM_001193489.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SECISBP2L	NM_001193489.2	c.203+885G>C		intron_variant	Intron 2 of 17	ENST00000559471.6	NP_001180418.1
SECISBP2L	NM_014701.4	c.203+885G>C		intron_variant	Intron 2 of 16		NP_055516.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SECISBP2L	ENST00000559471.6	c.203+885G>C		intron_variant	Intron 2 of 17	1	NM_001193489.2	ENSP00000453854.1
SECISBP2L	ENST00000261847.7	c.203+885G>C		intron_variant	Intron 2 of 16	1		ENSP00000261847.3
SECISBP2L	ENST00000380927.6	c.-310+885G>C		intron_variant	Intron 2 of 16	1		ENSP00000370314.2
SECISBP2L	ENST00000559424.1	c.203+885G>C		intron_variant	Intron 2 of 8	1		ENSP00000452987.1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78820 AN: 152012 Hom.: 22301 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.518 AC: 78863 AN: 152130 Hom.: 22311 Cov.: 33 AF XY: 0.521 AC XY: 38754 AN XY: 74358

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.536

Alfa AF: 0.580 Hom.: 3204

Bravo AF: 0.492

Asia WGS AF: 0.477 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.59

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: rs877007; hg19: chr15-49328903;