dbSNP rs4247039: TMEM179:c.522+36988C>T (chr14-104558177-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 ENST00000415614.6(TMEM179):c.522+36988C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,204 control chromosomes in the GnomAD database, including 3,807 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 0.21 ( 3807 hom., cov: 33)

Consequence

TMEM179
ENST00000415614.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.501

Publications

2 publications found

Variant links:

Genes affected

TMEM179 (HGNC:20137): (transmembrane protein 179) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM179 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM179	ENST00000415614.6 link	c.522+36988C>T		intron_variant	Intron 3 of 3	4		ENSP00000397763.2		I3L0F2

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31458

AN:

152084

Hom.:

3797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.0917

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.153

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.196

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.207

AC:

31497

AN:

152204

Hom.:

3807

Cov.:

AF XY:

0.210

AC XY:

15663

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.224

AC:

9297

AN:

41548

American (AMR)

AF:

0.262

AC:

4008

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0917

AC:

318

AN:

3468

East Asian (EAS)

AF:

0.599

AC:

3094

AN:

5168

South Asian (SAS)

AF:

0.281

AC:

1356

AN:

4824

European-Finnish (FIN)

AF:

0.153

AC:

1624

AN:

10610

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11295

AN:

67994

Other (OTH)

AF:

0.202

AC:

426

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1280

2560

3839

5119

6399

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<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:

0.196

Hom.:

1532

Bravo

AF:

0.221

Asia WGS

AF:

0.426

AC:

1481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.19

(source)

DANN

Benign

0.51

PhyloP100

-0.50

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over