Genetic Variant TEX41:n.308-26926T>C (chr2-145043894-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000445791.5(TEX41):n.308-26926T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,994 control chromosomes in the GnomAD database, including 27,397 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 0.58 ( 27396 hom., cov: 32)

Exomes 𝑓: 0.36 ( 1 hom. )

Consequence

TEX41
ENST00000445791.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.54

Publications

65 publications found

Variant links:

Genes affected

TEX41 (HGNC:48667): (testis expressed 41)

TEX41 links:

LOC100505498 (HGNC:):

LOC100505498 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 = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX41	NR_033870.2 link	n.464-26926T>C		intron_variant	Intron 3 of 4
LOC100505498	XR_923410.3 link	n.5785+20621T>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TEX41	ENST00000445791.5 link	n.308-26926T>C	intron_variant	Intron 2 of 3	1
TEX41	ENST00000451774.5 link	n.405-26926T>C	intron_variant	Intron 3 of 4	1
TEX41	ENST00000597173.6 link	n.433+20621T>C	intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87710

AN:

151864

Hom.:

27348

Cov.:

show subpopulations

Gnomad AFR

AF:

0.812

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.567

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.789

Gnomad SAS

AF:

0.628

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.562

GnomAD4 exome

AF:

0.357

AC:

AN:

Hom.:

Cov.:

AF XY:

0.357

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.400

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.578

AC:

87817

AN:

151980

Hom.:

27396

Cov.:

AF XY:

0.579

AC XY:

42957

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.812

AC:

33672

AN:

41476

American (AMR)

AF:

0.567

AC:

8643

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.411

AC:

1425

AN:

3470

East Asian (EAS)

AF:

0.789

AC:

4062

AN:

5146

South Asian (SAS)

AF:

0.627

AC:

3017

AN:

4810

European-Finnish (FIN)

AF:

0.416

AC:

4386

AN:

10542

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.452

AC:

30717

AN:

67970

Other (OTH)

AF:

0.567

AC:

1198

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1748

3496

5243

6991

8739

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.493

Hom.:

81218

Bravo

AF:

0.598

Asia WGS

AF:

0.704

AC:

2448

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.071

(source)

DANN

Benign

0.44

PhyloP100

-4.5

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over