rs11638981

chr15-49029332-T-Cchr15-49029332-T-G

Variant summary

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

The NM_001193489.2(SECISBP2L):c.665-650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,194 control chromosomes in the GnomAD database, including 3,904 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 0.20 (3904 hom., cov: 32)
• Consequence: SECISBP2L NM_001193489.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SECISBP2L	NM_001193489.2	c.665-650A>G		intron_variant		ENST00000559471.6
SECISBP2L	NM_014701.4	c.665-650A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SECISBP2L	ENST00000559471.6	c.665-650A>G		intron_variant		1	NM_001193489.2	P4
SECISBP2L	ENST00000261847.7	c.665-650A>G		intron_variant		1		A1
SECISBP2L	ENST00000380927.6	c.-50-650A>G		intron_variant		1
SECISBP2L	ENST00000559424.1	c.611-845A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31015 AN: 152076 Hom.: 3903 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.204 AC: 31014 AN: 152194 Hom.: 3904 Cov.: 32 AF XY: 0.207 AC XY: 15392 AN XY: 74404

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.229

Alfa AF: 0.251 Hom.: 8057

Bravo AF: 0.189

Asia WGS AF: 0.219 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.2
Dann	Benign	0.57

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: rs11638981; hg19: chr15-49321529;