Variant 1-108885722-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_013296.5(GPSM2):c.56+145dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 648,348 control chromosomes in the GnomAD database, including 783 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.053 ( 246 hom., cov: 32)

Exomes 𝑓: 0.040 ( 537 hom. )

Consequence

GPSM2
NM_013296.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.587

Variant links:

Genes affected

GPSM2 (HGNC:29501): (G protein signaling modulator 2) The protein encoded by this gene belongs to a family of proteins that modulate activation of G proteins, which transduce extracellular signals received by cell surface receptors into integrated cellular responses. The N-terminal half of this protein contains 10 copies of leu-gly-asn (LGN) repeat, and the C-terminal half contains 4 GoLoco motifs, which are involved in guanine nucleotide exchange. This protein may play a role in neuroblast division and in the development of normal hearing. Mutations in this gene are associated with autosomal recessive nonsyndromic deafness (DFNB82). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

GPSM2 links:

AKNAD1 (HGNC:28398): (AKNA domain containing 1) This gene encodes a protein which contains a domain found in an AT-hook-containing transcription factor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

AKNAD1 links:

CLCC1 (HGNC:29675): (chloride channel CLIC like 1) Predicted to enable chloride channel activity. Predicted to be involved in chloride transport. Located in endoplasmic reticulum and mitochondria-associated endoplasmic reticulum membrane. Implicated in retinitis pigmentosa 32. [provided by Alliance of Genome Resources, Apr 2022]

CLCC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-108885722-G-GT is Benign according to our data. Variant chr1-108885722-G-GT is described in ClinVar as [Benign]. Clinvar id is 1265073.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPSM2	NM_013296.5 linkuse as main transcript	c.56+145dup		intron_variant		ENST00000264126.9	NP_037428.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPSM2	ENST00000264126.9 linkuse as main transcript	c.56+145dup		intron_variant		1	NM_013296.5	ENSP00000264126	P1

Frequencies

GnomAD3 genomes

AF:

0.0528

AC:

8020

AN:

151986

Hom.:

242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0869

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.0302

Gnomad ASJ

AF:

0.00750

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0459

Gnomad FIN

AF:

0.0340

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0468

Gnomad OTH

AF:

0.0475

GnomAD4 exome

AF:

0.0403

AC:

20019

AN:

496244

Hom.:

537

AF XY:

0.0408

AC XY:

10888

AN XY:

266978

show subpopulations

Gnomad4 AFR exome

AF:

0.0880

Gnomad4 AMR exome

AF:

0.0235

Gnomad4 ASJ exome

AF:

0.0108

Gnomad4 EAS exome

AF:

0.000593

Gnomad4 SAS exome

AF:

0.0486

Gnomad4 FIN exome

AF:

0.0342

Gnomad4 NFE exome

AF:

0.0451

Gnomad4 OTH exome

AF:

0.0416

GnomAD4 genome

AF:

0.0529

AC:

8045

AN:

152104

Hom.:

246

Cov.:

AF XY:

0.0521

AC XY:

3872

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.0871

Gnomad4 AMR

AF:

0.0302

Gnomad4 ASJ

AF:

0.00750

Gnomad4 EAS

AF:

0.000773

Gnomad4 SAS

AF:

0.0459

Gnomad4 FIN

AF:

0.0340

Gnomad4 NFE

AF:

0.0468

Gnomad4 OTH

AF:

0.0494

Alfa

AF:

0.0498

Hom.:

Bravo

AF:

0.0536

Asia WGS

AF:

0.0400

AC:

140

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 29, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over