Variant rs2292181 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_144638.3(TMEM42):c.18G>C(p.Gly6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 1,420,196 control chromosomes in the GnomAD database, including 1,794 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 0.054 ( 234 hom., cov: 33)

Exomes 𝑓: 0.048 ( 1560 hom. )

Consequence

TMEM42
NM_144638.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

TMEM42 (HGNC:28444): (transmembrane protein 42) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM42 links:

MIR564 (HGNC:32820): (microRNA 564) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR564 links:

KIF15 (HGNC:17273): (kinesin family member 15) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in microtubule-based movement. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

KIF15 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP7

Synonymous conserved (PhyloP=1.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TMEM42	NM_144638.3 linkuse as main transcript	c.18G>C	p.Gly6=	synonymous_variant	1/3	ENST00000302392.5	NP_653239.1
MIR564	NR_030290.1 linkuse as main transcript	n.55G>C		non_coding_transcript_exon_variant	1/1
KIF15	XR_007095708.1 linkuse as main transcript	n.4368-6549G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TMEM42	ENST00000302392.5 linkuse as main transcript	c.18G>C	p.Gly6=	synonymous_variant	1/3	1	NM_144638.3	ENSP00000306564	P1
MIR564	ENST00000385049.1 linkuse as main transcript	n.55G>C		non_coding_transcript_exon_variant	1/1
TMEM42	ENST00000477126.1 linkuse as main transcript	n.39G>C		non_coding_transcript_exon_variant	1/2	1
KIF15	ENST00000422209.1 linkuse as main transcript	c.*59+9148G>C		intron_variant, NMD_transcript_variant		3		ENSP00000391205

Frequencies

GnomAD3 genomes

AF:

0.0539

AC:

8196

AN:

152172

Hom.:

234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0526

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0748

Gnomad ASJ

AF:

0.0513

Gnomad EAS

AF:

0.0544

Gnomad SAS

AF:

0.0436

Gnomad FIN

AF:

0.0345

Gnomad MID

AF:

0.0892

Gnomad NFE

AF:

0.0536

Gnomad OTH

AF:

0.0688

GnomAD3 exomes

AF:

0.0528

AC:

1798

AN:

34078

Hom.:

AF XY:

0.0510

AC XY:

1015

AN XY:

19900

show subpopulations

Gnomad AFR exome

AF:

0.0534

Gnomad AMR exome

AF:

0.0696

Gnomad ASJ exome

AF:

0.0688

Gnomad EAS exome

AF:

0.0440

Gnomad SAS exome

AF:

0.0453

Gnomad FIN exome

AF:

0.0400

Gnomad NFE exome

AF:

0.0510

Gnomad OTH exome

AF:

0.0586

GnomAD4 exome

AF:

0.0484

AC:

61392

AN:

1267912

Hom.:

1560

Cov.:

AF XY:

0.0487

AC XY:

30112

AN XY:

618742

show subpopulations

Gnomad4 AFR exome

AF:

0.0519

Gnomad4 AMR exome

AF:

0.0741

Gnomad4 ASJ exome

AF:

0.0565

Gnomad4 EAS exome

AF:

0.0469

Gnomad4 SAS exome

AF:

0.0441

Gnomad4 FIN exome

AF:

0.0388

Gnomad4 NFE exome

AF:

0.0481

Gnomad4 OTH exome

AF:

0.0507

GnomAD4 genome

AF:

0.0539

AC:

8208

AN:

152284

Hom.:

234

Cov.:

AF XY:

0.0533

AC XY:

3969

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0527

Gnomad4 AMR

AF:

0.0747

Gnomad4 ASJ

AF:

0.0513

Gnomad4 EAS

AF:

0.0545

Gnomad4 SAS

AF:

0.0437

Gnomad4 FIN

AF:

0.0345

Gnomad4 NFE

AF:

0.0536

Gnomad4 OTH

AF:

0.0681

Alfa

AF:

0.0575

Hom.:

Bravo

AF:

0.0556

Asia WGS

AF:

0.0470

AC:

165

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.8

DANN

Benign

0.55

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over