Variant chr14-105529712-T-TGCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_025268.4(TMEM121):c.896_898dupCGC(p.Pro299dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0016 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0022 ( 6 hom. )

Consequence

TMEM121
NM_025268.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.501

Variant links:

Genes affected

TMEM121 (HGNC:20511): (transmembrane protein 121) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM121 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM121	NM_025268.4 linkuse as main transcript	c.896_898dupCGC	p.Pro299dup	disruptive_inframe_insertion	2/2	ENST00000392519.7	NP_079544.1	Q9BTD3
TMEM121	NM_001331238.2 linkuse as main transcript	c.896_898dupCGC	p.Pro299dup	disruptive_inframe_insertion	2/2		NP_001318167.1	Q9BTD3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM121	ENST00000392519.7 linkuse as main transcript	c.896_898dupCGC	p.Pro299dup	disruptive_inframe_insertion	2/2	1	NM_025268.4	ENSP00000376304.2		Q9BTD3

Frequencies

GnomAD3 genomes

AF:

0.00162

AC:

246

AN:

151668

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000170

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.00448

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00209

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.00194

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00191

AC:

227

AN:

118980

Hom.:

AF XY:

0.00196

AC XY:

129

AN XY:

65840

show subpopulations

Gnomad AFR exome

AF:

0.000405

Gnomad AMR exome

AF:

0.00108

Gnomad ASJ exome

AF:

0.00678

Gnomad EAS exome

AF:

0.00282

Gnomad SAS exome

AF:

0.00135

Gnomad FIN exome

AF:

0.00305

Gnomad NFE exome

AF:

0.00157

Gnomad OTH exome

AF:

0.00219

GnomAD4 exome

AF:

0.00224

AC:

3088

AN:

1375870

Hom.:

Cov.:

AF XY:

0.00231

AC XY:

1566

AN XY:

678932

show subpopulations

Gnomad4 AFR exome

AF:

0.000131

Gnomad4 AMR exome

AF:

0.000720

Gnomad4 ASJ exome

AF:

0.00770

Gnomad4 EAS exome

AF:

0.00227

Gnomad4 SAS exome

AF:

0.00171

Gnomad4 FIN exome

AF:

0.00400

Gnomad4 NFE exome

AF:

0.00223

Gnomad4 OTH exome

AF:

0.00181

GnomAD4 genome

AF:

0.00161

AC:

245

AN:

151776

Hom.:

Cov.:

AF XY:

0.00167

AC XY:

124

AN XY:

74188

show subpopulations

Gnomad4 AFR

AF:

0.000169

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.00449

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00209

Gnomad4 NFE

AF:

0.00195

Gnomad4 OTH

AF:

0.00427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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