dbSNP rs9854612: TMED10P2:n.352G>A (chr3-128538371-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000474255.1(TMED10P2):n.352G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 583,758 control chromosomes in the GnomAD database, including 38,054 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 0.40 ( 13722 hom., cov: 32)

Exomes 𝑓: 0.32 ( 24332 hom. )

Consequence

TMED10P2
ENST00000474255.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Publications

6 publications found

Variant links:

Genes affected

TMED10P2 (HGNC:38105): (transmembrane p24 trafficking protein 10 pseudogene 2)

TMED10P2 links:

GATA2-AS1 (HGNC:51108): (GATA2 antisense RNA 1)

GATA2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMED10P2		n.128538371G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TMED10P2	ENST00000474255.1 link	n.352G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
GATA2-AS1	ENST00000740166.1 link	n.740G>A	non_coding_transcript_exon_variant	Exon 3 of 3
GATA2-AS1	ENST00000740167.1 link	n.668G>A	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.401

AC:

60914

AN:

151832

Hom.:

13688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.601

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.425

Gnomad ASJ

AF:

0.403

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.270

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.395

GnomAD4 exome

AF:

0.325

AC:

140241

AN:

431806

Hom.:

24332

Cov.:

AF XY:

0.321

AC XY:

75963

AN XY:

236434

show subpopulations

African (AFR)

AF:

0.605

AC:

6929

AN:

11448

American (AMR)

AF:

0.437

AC:

11673

AN:

26698

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

4521

AN:

11112

East Asian (EAS)

AF:

0.461

AC:

9307

AN:

20198

South Asian (SAS)

AF:

0.301

AC:

16353

AN:

54240

European-Finnish (FIN)

AF:

0.268

AC:

5343

AN:

19964

Middle Eastern (MID)

AF:

0.424

AC:

1304

AN:

3072

European-Non Finnish (NFE)

AF:

0.294

AC:

77541

AN:

263762

Other (OTH)

AF:

0.341

AC:

7270

AN:

21312

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

4252

8504

12755

17007

21259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1188

2376

3564

4752

5940

<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:

0.402

AC:

61011

AN:

151952

Hom.:

13722

Cov.:

AF XY:

0.400

AC XY:

29738

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.601

AC:

24915

AN:

41438

American (AMR)

AF:

0.425

AC:

6487

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.403

AC:

1396

AN:

3468

East Asian (EAS)

AF:

0.463

AC:

2393

AN:

5168

South Asian (SAS)

AF:

0.305

AC:

1473

AN:

4822

European-Finnish (FIN)

AF:

0.270

AC:

2854

AN:

10558

Middle Eastern (MID)

AF:

0.455

AC:

133

AN:

292

European-Non Finnish (NFE)

AF:

0.297

AC:

20195

AN:

67930

Other (OTH)

AF:

0.397

AC:

836

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1732

3465

5197

6930

8662

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

548

1096

1644

2192

2740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.322

Hom.:

13384

Bravo

AF:

0.427

Asia WGS

AF:

0.398

AC:

1385

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

1.2

(source)

DANN

Benign

0.67

PhyloP100

-1.5

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over