dbSNP rs955944: TEX41:n.308-15226A>C (chr2-145055594-A-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.308-15226A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 152,258 control chromosomes in the GnomAD database, including 210 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 0.018 ( 210 hom., cov: 32)

Consequence

TEX41
ENST00000445791.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.351

Publications

3 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX41	NR_033870.2 link	n.464-15226A>C		intron_variant	Intron 3 of 4
LOC100505498	XR_923410.3 link	n.5785+32321A>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TEX41	ENST00000445791.5 link	n.308-15226A>C	intron_variant	Intron 2 of 3	1
TEX41	ENST00000451774.5 link	n.405-15226A>C	intron_variant	Intron 3 of 4	1
TEX41	ENST00000597173.6 link	n.433+32321A>C	intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.0183

AC:

2788

AN:

152140

Hom.:

211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00309

Gnomad AMI

AF:

0.0493

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0892

Gnomad SAS

AF:

0.00415

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.0229

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

GnomAD4 genome

AF:

0.0183

AC:

2787

AN:

152258

Hom.:

210

Cov.:

AF XY:

0.0204

AC XY:

1517

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.00308

AC:

128

AN:

41570

American (AMR)

AF:

0.135

AC:

2069

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.0892

AC:

462

AN:

5178

South Asian (SAS)

AF:

0.00373

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000235

AC:

AN:

68014

Other (OTH)

AF:

0.0232

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

125

251

376

502

627

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<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:

0.0291

Hom.:

177

Bravo

AF:

0.0309

Asia WGS

AF:

0.0310

AC:

109

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.2

(source)

DANN

Benign

0.53

PhyloP100

0.35

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over