dbSNP rs2304264: TEX36-AS1:n.508G>A (chr10-125576346-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 ENST00000446081.5(TEX36-AS1):n.508G>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 0.0702 in 177,178 control chromosomes in the GnomAD database, including 649 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 0.068 ( 530 hom., cov: 33)

Exomes 𝑓: 0.082 ( 119 hom. )

Consequence

TEX36-AS1
ENST00000446081.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.206

Publications

3 publications found

Variant links:

Genes affected

TEX36-AS1 (HGNC:49500): (TEX36 antisense RNA 1)

TEX36-AS1 links:

TEX36 (HGNC:31653): (testis expressed 36)

TEX36 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX36-AS1	NR_023362.1 link	n.508G>A		non_coding_transcript_exon_variant	Exon 4 of 5
TEX36	NM_001318133.2 link	c.*403C>T		downstream_gene_variant			NP_001305062.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TEX36-AS1	ENST00000446081.5 link	n.508G>A	non_coding_transcript_exon_variant	Exon 4 of 5	1
TEX36-AS1	ENST00000816071.1 link	n.396G>A	non_coding_transcript_exon_variant	Exon 3 of 4
TEX36-AS1	ENST00000816072.1 link	n.266G>A	non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0683

AC:

10396

AN:

152190

Hom.:

527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0171

Gnomad AMI

AF:

0.0462

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.0421

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.0306

Gnomad FIN

AF:

0.0865

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0804

Gnomad OTH

AF:

0.0774

GnomAD4 exome

AF:

0.0817

AC:

2033

AN:

24870

Hom.:

119

Cov.:

AF XY:

0.0819

AC XY:

1049

AN XY:

12804

show subpopulations

African (AFR)

AF:

0.00873

AC:

AN:

1260

American (AMR)

AF:

0.151

AC:

452

AN:

2992

Ashkenazi Jewish (ASJ)

AF:

0.0298

AC:

AN:

604

East Asian (EAS)

AF:

0.153

AC:

294

AN:

1926

South Asian (SAS)

AF:

0.0218

AC:

AN:

2248

European-Finnish (FIN)

AF:

0.0720

AC:

AN:

528

Middle Eastern (MID)

AF:

0.0135

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0773

AC:

1087

AN:

14064

Other (OTH)

AF:

0.0707

AC:

AN:

1174

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

195

292

390

487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.0683

AC:

10402

AN:

152308

Hom.:

530

Cov.:

AF XY:

0.0695

AC XY:

5180

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.0171

AC:

709

AN:

41566

American (AMR)

AF:

0.126

AC:

1925

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0421

AC:

146

AN:

3472

East Asian (EAS)

AF:

0.168

AC:

872

AN:

5178

South Asian (SAS)

AF:

0.0309

AC:

149

AN:

4826

European-Finnish (FIN)

AF:

0.0865

AC:

918

AN:

10618

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0804

AC:

5473

AN:

68030

Other (OTH)

AF:

0.0776

AC:

164

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

495

991

1486

1982

2477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0728

Hom.:

1091

Bravo

AF:

0.0719

Asia WGS

AF:

0.0850

AC:

294

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.0

(source)

DANN

Benign

0.74

PhyloP100

-0.21

Mutation Taster

=100/0

polymorphism (auto)

(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