Variant chr15-44379729-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_138423.4(GOLM2):c.842G>T(p.Ser281Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,422,264 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 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: 31)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

GOLM2
NM_138423.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.171

Variant links:

Genes affected

GOLM2 (HGNC:24892): (golgi membrane protein 2) The increased expression level of this gene is associated with HER-2/neu proto-oncogene overexpression. Amplification and resulting overexpression of this proto-oncogene are found in approximately 30% of human breast and 20% of human ovarian cancers. Alternatively spliced variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Dec 2010]

GOLM2 links:

GOLM2 (HGNC:):

GOLM2 links:

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ACMG classification

Classification made for transcript

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=0.14311323).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
GOLM2	NM_138423.4 linkuse as main transcript	c.842G>T	p.Ser281Ile	missense_variant	7/10	ENST00000299957.11	NP_612432.2
GOLM2	NM_177974.3 linkuse as main transcript	c.842G>T	p.Ser281Ile	missense_variant	7/9		NP_816929.1
GOLM2	NR_157849.2 linkuse as main transcript	n.2545G>T		non_coding_transcript_exon_variant	8/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GOLM2	ENST00000299957.11 linkuse as main transcript	c.842G>T	p.Ser281Ile	missense_variant	7/10	1	NM_138423.4	ENSP00000299957.6	Q6P4E1-4
GOLM2	ENST00000345795.6 linkuse as main transcript	c.842G>T	p.Ser281Ile	missense_variant	7/9	1		ENSP00000335063.4	Q6P4E1-2
GOLM2	ENST00000650436.1 linkuse as main transcript	c.485G>T	p.Ser162Ile	missense_variant	9/12			ENSP00000496905.1	A0A3B3IRW9
GOLM2	ENST00000558847.1 linkuse as main transcript	c.182G>T	p.Ser61Ile	missense_variant	2/4	3		ENSP00000453465.1	H0YM51

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000141

AC:

AN:

1422264

Hom.:

Cov.:

AF XY:

0.00000283

AC XY:

AN XY:

707276

show subpopulations

Gnomad4 AFR exome

AF:

0.0000311

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000174

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 07, 2024

The c.842G>T (p.S281I) alteration is located in exon 7 (coding exon 7) of the CASC4 gene. This alteration results from a G to T substitution at nucleotide position 842, causing the serine (S) at amino acid position 281 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.079

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.97

Eigen

Benign

-0.074

Eigen_PC

Benign

-0.053

FATHMM_MKL

Benign

0.61

LIST_S2

Benign

0.41

T;T;T

M_CAP

Benign

0.0075

MetaRNN

Benign

0.14

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

L;.;L

PrimateAI

Benign

0.30

PROVEAN

Benign

-1.8

N;.;N

REVEL

Benign

0.048

Sift

Uncertain

0.0070

D;.;D

Sift4G

Benign

0.062

T;.;T

Polyphen

0.63

.;.;P

Vest4

0.16

MutPred

0.25

Loss of phosphorylation at S281 (P = 0.0493);.;Loss of phosphorylation at S281 (P = 0.0493);

MVP

0.28

MPC

0.70

ClinPred

0.39

GERP RS

1.2

gMVP

0.25

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over