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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_025268.4(TMEM121):c.896_898delCGC(p.Pro299del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,524,964 control chromosomes in the GnomAD database, including 66,989 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 13184 hom., cov: 0)

Exomes 𝑓: 0.27 ( 53805 hom. )

Consequence

TMEM121
NM_025268.4 disruptive_inframe_deletion

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 Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM121	NM_025268.4 link	c.896_898delCGC	p.Pro299del	disruptive_inframe_deletion	2/2	ENST00000392519.7	NP_079544.1	Q9BTD3
TMEM121	NM_001331238.2 link	c.896_898delCGC	p.Pro299del	disruptive_inframe_deletion	2/2		NP_001318167.1	Q9BTD3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM121	ENST00000392519.7 link	c.896_898delCGC	p.Pro299del	disruptive_inframe_deletion	2/2	1	NM_025268.4	ENSP00000376304.2		Q9BTD3

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57185

AN:

151606

Hom.:

13129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.650

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.494

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.293

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.338

GnomAD3 exomes

AF:

0.299

AC:

35606

AN:

118980

Hom.:

6254

AF XY:

0.299

AC XY:

19684

AN XY:

65840

show subpopulations

Gnomad AFR exome

AF:

0.691

Gnomad AMR exome

AF:

0.199

Gnomad ASJ exome

AF:

0.339

Gnomad EAS exome

AF:

0.546

Gnomad SAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.296

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.285

GnomAD4 exome

AF:

0.271

AC:

371787

AN:

1373250

Hom.:

53805

AF XY:

0.270

AC XY:

182936

AN XY:

677610

show subpopulations

Gnomad4 AFR exome

AF:

0.672

Gnomad4 AMR exome

AF:

0.196

Gnomad4 ASJ exome

AF:

0.337

Gnomad4 EAS exome

AF:

0.395

Gnomad4 SAS exome

AF:

0.261

Gnomad4 FIN exome

AF:

0.296

Gnomad4 NFE exome

AF:

0.254

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.378

AC:

57287

AN:

151714

Hom.:

13184

Cov.:

AF XY:

0.374

AC XY:

27719

AN XY:

74158

show subpopulations

Gnomad4 AFR

AF:

0.651

Gnomad4 AMR

AF:

0.237

Gnomad4 ASJ

AF:

0.351

Gnomad4 EAS

AF:

0.493

Gnomad4 SAS

AF:

0.250

Gnomad4 FIN

AF:

0.305

Gnomad4 NFE

AF:

0.260

Gnomad4 OTH

AF:

0.344

Bravo

AF:

0.390

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over