rs137957961

Variant names:

• chr12-75391333-T-A
• rs137957961
• NM_001270396.2:c.217T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-75391333-T-A
• chr12-75391333-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001270396.2(GLIPR1L2):​c.217T>A​(p.Ser73Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GLIPR1L2 NM_001270396.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684

Genes affected

GLIPR1L2 (HGNC:28592): (GLIPR1 like 2) This gene encodes a member of the cysteine-rich secretory protein, antigen 5, and pathogenesis-related 1 superfamily. Members of this family have roles in a variety of processes, including cancer and immune defense. This gene is located in a cluster with two related genes on chromosome 12. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2622227).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLIPR1L2	NM_001270396.2	c.217T>A	p.Ser73Thr	missense_variant	Exon 1 of 6	ENST00000550916.6	NP_001257325.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLIPR1L2	ENST00000550916.6	c.217T>A	p.Ser73Thr	missense_variant	Exon 1 of 6	1	NM_001270396.2	ENSP00000448248.1
GLIPR1L2	ENST00000320460.8	c.217T>A	p.Ser73Thr	missense_variant	Exon 1 of 4	1		ENSP00000317385.4
GLIPR1L2	ENST00000378692	c.-235T>A		5_prime_UTR_variant	Exon 1 of 7	1		ENSP00000367963.3
GLIPR1L2	ENST00000547164.1	c.217T>A	p.Ser73Thr	missense_variant	Exon 1 of 3	5		ENSP00000447980.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	14
DANN	Benign	0.88
DEOGEN2	Benign	0.013	T;.;.
Eigen	Benign	-0.79
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.023	N
LIST_S2	Benign	0.63	T;T;T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.26	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.1	M;M;M
PrimateAI	Benign	0.44	T
PROVEAN	Benign	-1.8	N;N;N
REVEL	Benign	0.049
Sift	Benign	0.15	T;T;T
Sift4G	Uncertain	0.017	D;T;T
Polyphen		0.61	P;P;.
Vest4		0.20
MutPred		0.57		Gain of catalytic residue at R71 (P = 0.004);Gain of catalytic residue at R71 (P = 0.004);Gain of catalytic residue at R71 (P = 0.004);
MVP		0.26
MPC		0.080
ClinPred		0.36	T
GERP RS		-3.6
Varity_R		0.10
gMVP		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: rs137957961; hg19: chr12-75785113;