chr12-75343862-C-A

Variant names:

• chr12-75343862-C-A
• rs180934864
• NM_001304964.2:c.344C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001304964.2(GLIPR1L1):​c.344C>A​(p.Thr115Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,459,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T115M) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: GLIPR1L1 NM_001304964.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.11
• Publications: 2 publications found

Genes affected

GLIPR1L1 (HGNC:28392): (GLIPR1 like 1) Predicted to be involved in single fertilization. Predicted to act upstream of or within binding activity of sperm to zona pellucida. Predicted to be located in sperm connecting piece. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

CAPS2 (HGNC:16471): (calcyphosine 2) Calcyphosine-2 is a calcium-binding protein with 2 EF-hand motifs (Wang et al., 2002 [PubMed 11846421]).[supplied by OMIM, Mar 2008]

CAPS2 Gene-Disease associations (from GenCC):

• intellectual disability

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06021762).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304964.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLIPR1L1	NM_001304964.2	MANE Select	c.344C>A	p.Thr115Lys	missense	Exon 2 of 6	NP_001291893.1	Q6UWM5-1
	GLIPR1L1	NM_152779.4		c.344C>A	p.Thr115Lys	missense	Exon 2 of 5	NP_689992.1	Q6UWM5-2
	CAPS2	NM_001355023.4		c.-29-17335G>T		intron	N/A	NP_001341952.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLIPR1L1	ENST00000378695.9	TSL:1 MANE Select	c.344C>A	p.Thr115Lys	missense	Exon 2 of 6	ENSP00000367967.4	Q6UWM5-1
	GLIPR1L1	ENST00000312442.2	TSL:1	c.344C>A	p.Thr115Lys	missense	Exon 2 of 5	ENSP00000310770.2	Q6UWM5-2
	CAPS2	ENST00000328705.7	TSL:1	n.*372-18574G>T		intron	N/A	ENSP00000331007.3	H7BXT1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000343 AC: 5 AN: 1459432 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 726186

African (AFR) AF: 0.00 AC: 0 AN: 33414

American (AMR) AF: 0.00 AC: 0 AN: 44706

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26104

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39606

South Asian (SAS) AF: 0.00 AC: 0 AN: 86182

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53402

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5752

European-Non Finnish (NFE) AF: 0.00000360 AC: 4 AN: 1109960

Other (OTH) AF: 0.00 AC: 0 AN: 60306

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.0010
DANN	Benign	0.36
DEOGEN2	Benign	0.033	T
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.0090	N
LIST_S2	Benign	0.15	T
M_CAP	Benign	0.0053	T
MetaRNN	Benign	0.060	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.18	N
PhyloP100		-7.1
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.037
Sift	Benign	0.34	T
Sift4G	Benign	1.0	T
Polyphen		0.010	B
Vest4		0.15
MutPred		0.55		Gain of catalytic residue at A116 (P = 0)
MVP		0.040
MPC		0.038
ClinPred		0.17	T
GERP RS		-9.7
Varity_R		0.085
gMVP		0.45
Mutation Taster		=91/9	polymorphism

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: rs180934864; hg19: chr12-75737642;