Genetic Variant TMEM121:p.Pro298_Pro299del (chr14-105529712-TGCCGCC-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_025268.4(TMEM121):c.893_898delCGCCGC(p.Pro298_Pro299del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000236 in 1,526,926 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000040 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000022 ( 0 hom. )

Consequence

TMEM121
NM_025268.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.00

Publications

18 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025268.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM121	NM_025268.4	MANE Select	c.893_898delCGCCGC	p.Pro298_Pro299del	disruptive_inframe_deletion	Exon 2 of 2	NP_079544.1
	TMEM121	NM_001331238.2		c.893_898delCGCCGC	p.Pro298_Pro299del	disruptive_inframe_deletion	Exon 2 of 2	NP_001318167.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
TMEM121	ENST00000392519.7	TSL:1 MANE Select	c.893_898delCGCCGC	p.Pro298_Pro299del	disruptive_inframe_deletion	Exon 2 of 2	ENSP00000376304.2
TMEM121	ENST00000903730.1		c.893_898delCGCCGC	p.Pro298_Pro299del	disruptive_inframe_deletion	Exon 2 of 2	ENSP00000573789.1
TMEM121	ENST00000903731.1		c.893_898delCGCCGC	p.Pro298_Pro299del	disruptive_inframe_deletion	Exon 2 of 2	ENSP00000573790.1

Frequencies

GnomAD3 genomes

AF:

0.0000396

AC:

AN:

151668

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000442

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000420

AC:

AN:

118980

AF XY:

0.0000152

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000451

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000274

GnomAD4 exome

AF:

0.0000218

AC:

AN:

1375150

Hom.:

AF XY:

0.0000147

AC XY:

AN XY:

678570

show subpopulations

African (AFR)

AF:

0.0000659

AC:

AN:

30330

American (AMR)

AF:

0.0000577

AC:

AN:

34692

Ashkenazi Jewish (ASJ)

AF:

0.0000406

AC:

AN:

24652

East Asian (EAS)

AF:

0.0000285

AC:

AN:

35114

South Asian (SAS)

AF:

0.000153

AC:

AN:

78342

European-Finnish (FIN)

AF:

0.0000292

AC:

AN:

34246

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5372

European-Non Finnish (NFE)

AF:

0.00000930

AC:

AN:

1075022

Other (OTH)

AF:

0.0000174

AC:

AN:

57380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.405

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000395

AC:

AN:

151776

Hom.:

Cov.:

AF XY:

0.0000404

AC XY:

AN XY:

74188

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41372

American (AMR)

AF:

0.00

AC:

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5118

South Asian (SAS)

AF:

0.000621

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10540

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0000442

AC:

AN:

67860

Other (OTH)

AF:

0.00

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.000338

Hom.:

666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

5.0

Mutation Taster

=186/14

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over