dbSNP rs5030881: TMEM14DP:n.322C>T (chr10-68544512-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 ENST00000422205.1(TMEM14DP):n.322C>T 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 0.932 in 152,174 control chromosomes in the GnomAD database, including 66,253 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 0.93 ( 66253 hom., cov: 31)

Exomes 𝑓: 0.95 ( 625318 hom. )

Failed GnomAD Quality Control

Consequence

TMEM14DP
ENST00000422205.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

5 publications found

Variant links:

Genes affected

TMEM14DP (HGNC:15660): (transmembrane protein 14D, pseudogene) Predicted to be involved in mitochondrial transport. Predicted to be integral component of membrane. Predicted to be active in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM14DP links:

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new If you want to explore the variant's impact on the transcript ENST00000422205.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM14DP	ENST00000422205.1	TSL:6	n.322C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.932

AC:

141784

AN:

152056

Hom.:

66212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.879

Gnomad AMI

AF:

0.966

Gnomad AMR

AF:

0.914

Gnomad ASJ

AF:

0.957

Gnomad EAS

AF:

0.985

Gnomad SAS

AF:

0.911

Gnomad FIN

AF:

0.989

Gnomad MID

AF:

0.934

Gnomad NFE

AF:

0.957

Gnomad OTH

AF:

0.922

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.953

AC:

1311924

AN:

1376982

Hom.:

625318

Cov.:

AF XY:

0.952

AC XY:

656095

AN XY:

689400

show subpopulations

African (AFR)

AF:

0.881

AC:

27876

AN:

31646

American (AMR)

AF:

0.925

AC:

41204

AN:

44524

Ashkenazi Jewish (ASJ)

AF:

0.946

AC:

24214

AN:

25588

East Asian (EAS)

AF:

0.987

AC:

38719

AN:

39244

South Asian (SAS)

AF:

0.914

AC:

77169

AN:

84476

European-Finnish (FIN)

AF:

0.987

AC:

52527

AN:

53236

Middle Eastern (MID)

AF:

0.942

AC:

4485

AN:

4760

European-Non Finnish (NFE)

AF:

0.957

AC:

991347

AN:

1036144

Other (OTH)

AF:

0.948

AC:

54383

AN:

57364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

2742

5483

8225

10966

13708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19602

39204

58806

78408

98010

<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:

0.932

AC:

141876

AN:

152174

Hom.:

66253

Cov.:

AF XY:

0.933

AC XY:

69397

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.879

AC:

36462

AN:

41494

American (AMR)

AF:

0.914

AC:

13932

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.957

AC:

3322

AN:

3470

East Asian (EAS)

AF:

0.985

AC:

5108

AN:

5186

South Asian (SAS)

AF:

0.911

AC:

4395

AN:

4824

European-Finnish (FIN)

AF:

0.989

AC:

10485

AN:

10602

Middle Eastern (MID)

AF:

0.922

AC:

271

AN:

294

European-Non Finnish (NFE)

AF:

0.957

AC:

65072

AN:

68030

Other (OTH)

AF:

0.922

AC:

1948

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

490

980

1469

1959

2449

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.942

Hom.:

9619

Bravo

AF:

0.926

Asia WGS

AF:

0.922

AC:

3208

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

7.7

(source)

DANN

Benign

0.38

PhyloP100

-0.097

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over