dbSNP rs302873: TEX14:c.-183G>C (chr17-58692120-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_031272.5(TEX14):c.-183G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 72,160 control chromosomes in the GnomAD database, including 14,712 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 0.69 ( 14519 hom., cov: 9)

Exomes 𝑓: 0.37 ( 193 hom. )

Consequence

TEX14
NM_031272.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Publications

11 publications found

Variant links:

COSMIC-nc: COSV53618722

Genes affected

TEX14 (HGNC:11737): (testis expressed 14, intercellular bridge forming factor) The protein encoded by this gene is necessary for intercellular bridges in germ cells, which are required for spermatogenesis. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

TEX14 links:

IGBP1C (HGNC:43611): (IGBP1 family member C) Predicted to enable protein phosphatase 2A binding activity. Predicted to be involved in regulation of dephosphorylation. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

IGBP1C 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
TEX14	NM_031272.5 link	c.-183G>C	upstream_gene_variant	ENST00000349033.10	NP_112562.3
IGBP1C	NM_001395966.1 link	c.-412G>C	upstream_gene_variant	ENST00000583666.3	NP_001382895.1
TEX14	NM_001201457.2 link	c.-183G>C	upstream_gene_variant		NP_001188386.1
TEX14	NM_198393.4 link	c.-183G>C	upstream_gene_variant		NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10 link	c.-183G>C		upstream_gene_variant		5	NM_031272.5	ENSP00000268910.8
IGBP1C	ENST00000583666.3 link	c.-412G>C		upstream_gene_variant		3	NM_001395966.1	ENSP00000492384.1

Frequencies

GnomAD3 genomes

AF:

0.687

AC:

48269

AN:

70270

Hom.:

14507

Cov.:

show subpopulations

Gnomad AFR

AF:

0.730

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.684

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.681

Gnomad MID

AF:

0.732

Gnomad NFE

AF:

0.689

Gnomad OTH

AF:

0.664

GnomAD4 exome

AF:

0.365

AC:

693

AN:

1898

Hom.:

193

AF XY:

0.386

AC XY:

393

AN XY:

1018

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.222

AC:

105

AN:

472

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.342

AC:

AN:

260

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.439

AC:

466

AN:

1062

Other (OTH)

AF:

0.438

AC:

AN:

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

Age Distribution

Exome Het

Exome Hom

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:

0.687

AC:

48277

AN:

70262

Hom.:

14519

Cov.:

AF XY:

0.684

AC XY:

21786

AN XY:

31850

show subpopulations

African (AFR)

AF:

0.730

AC:

11562

AN:

15834

American (AMR)

AF:

0.613

AC:

3143

AN:

5126

Ashkenazi Jewish (ASJ)

AF:

0.684

AC:

1553

AN:

2270

East Asian (EAS)

AF:

0.550

AC:

928

AN:

1686

South Asian (SAS)

AF:

0.634

AC:

978

AN:

1542

European-Finnish (FIN)

AF:

0.681

AC:

1957

AN:

2874

Middle Eastern (MID)

AF:

0.750

AC:

117

AN:

156

European-Non Finnish (NFE)

AF:

0.689

AC:

27105

AN:

39330

Other (OTH)

AF:

0.665

AC:

633

AN:

952

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

744

1488

2232

2976

3720

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

380

760

1140

1520

1900

<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:

0.624

Hom.:

2759

Bravo

AF:

0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.61

(source)

DANN

Benign

0.097

PhyloP100

-1.1

PromoterAI

-0.059

Neutral

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over