rs11638981

Variant names:

• chr15-49029332-T-C
• rs11638981
• NM_001193489.2:c.665-650A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-49029332-T-C
• chr15-49029332-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SECISBP2L	NM_001193489.2	c.665-650A>G		intron_variant	Intron 4 of 17	ENST00000559471.6	NP_001180418.1
SECISBP2L	NM_014701.4	c.665-650A>G		intron_variant	Intron 4 of 16		NP_055516.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SECISBP2L	ENST00000559471.6	c.665-650A>G		intron_variant	Intron 4 of 17	1	NM_001193489.2	ENSP00000453854.1
SECISBP2L	ENST00000261847.7	c.665-650A>G		intron_variant	Intron 4 of 16	1		ENSP00000261847.3
SECISBP2L	ENST00000380927.6	c.-50-650A>G		intron_variant	Intron 4 of 16	1		ENSP00000370314.2
SECISBP2L	ENST00000559424.1	c.611-845A>G		intron_variant	Intron 4 of 8	1		ENSP00000452987.1

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

African (AFR) AF: 0.0578 AC: 2402 AN: 41554

American (AMR) AF: 0.210 AC: 3214 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1020 AN: 5174

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4818

European-Finnish (FIN) AF: 0.293 AC: 3100 AN: 10576

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18206 AN: 68002

Other (OTH) AF: 0.229 AC: 484 AN: 2114

Alfa AF: 0.236 Hom.: 11988

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
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11638981; hg19: chr15-49321529;