Genetic Variant ENST00000445791.5:n.308-136671G>A (chr2-144934149-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 ENST00000445791.5(TEX41):n.308-136671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,862 control chromosomes in the GnomAD database, including 27,821 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 0.60 ( 27821 hom., cov: 32)

Consequence

TEX41
ENST00000445791.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.400

Publications

4 publications found

Variant links:

Genes affected

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

TEX41 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 = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX41	NR_033870.2 link	n.463+30346G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TEX41	ENST00000445791.5 link	n.308-136671G>A	intron_variant	Intron 2 of 3	1
TEX41	ENST00000451774.5 link	n.404+30346G>A	intron_variant	Intron 3 of 4	1
TEX41	ENST00000451027.5 link	n.469-110217G>A	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.597

AC:

90523

AN:

151742

Hom.:

27809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.484

Gnomad AMI

AF:

0.721

Gnomad AMR

AF:

0.660

Gnomad ASJ

AF:

0.659

Gnomad EAS

AF:

0.977

Gnomad SAS

AF:

0.718

Gnomad FIN

AF:

0.615

Gnomad MID

AF:

0.596

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.573

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

GnomAD4 genome

AF:

0.596

AC:

90565

AN:

151862

Hom.:

27821

Cov.:

AF XY:

0.602

AC XY:

44678

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.484

AC:

20030

AN:

41404

American (AMR)

AF:

0.660

AC:

10058

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.659

AC:

2287

AN:

3470

East Asian (EAS)

AF:

0.978

AC:

5052

AN:

5168

South Asian (SAS)

AF:

0.719

AC:

3465

AN:

4820

European-Finnish (FIN)

AF:

0.615

AC:

6465

AN:

10510

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.606

AC:

41176

AN:

67950

Other (OTH)

AF:

0.573

AC:

1210

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1813

3626

5438

7251

9064

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<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:

0.600

Hom.:

3478

Bravo

AF:

0.595

Asia WGS

AF:

0.803

AC:

2788

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

0.95

(source)

DANN

Benign

0.56

PhyloP100

-0.40

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