Genetic Variant ENST00000331787.3:n.373-23161G>A (chrY-18956002-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000331787.3(TTTY14):n.373-23161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.59 ( 0 hom., 18419 hem., cov: 0)

Failed GnomAD Quality Control

Consequence

TTTY14
ENST00000331787.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

Publications

5 publications found

Variant links:

Genes affected

TTTY14 (HGNC:18495): (testis expressed transcript, Y-linked 14)

TTTY14 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TTTY14	NR_001543.4 link	n.504-23161G>A	intron_variant	Intron 1 of 1
TTTY14	NR_125733.1 link	n.579-22527G>A	intron_variant	Intron 2 of 4
TTTY14	NR_125734.1 link	n.579-78797G>A	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TTTY14	ENST00000331787.3 link	n.373-23161G>A	intron_variant	Intron 1 of 1	1
TTTY14	ENST00000452584.5 link	n.336-23161G>A	intron_variant	Intron 4 of 4	3
TTTY14	ENST00000454875.3 link	n.449-78797G>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.590

AC:

18341

AN:

31099

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.792

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.811

Gnomad EAS

AF:

0.996

Gnomad SAS

AF:

0.660

Gnomad FIN

AF:

0.935

Gnomad MID

AF:

0.956

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.562

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.591

AC:

18419

AN:

31168

Hom.:

Cov.:

AF XY:

0.591

AC XY:

18419

AN XY:

31168

show subpopulations

African (AFR)

AF:

0.793

AC:

6250

AN:

7878

American (AMR)

AF:

0.502

AC:

1681

AN:

3347

Ashkenazi Jewish (ASJ)

AF:

0.811

AC:

597

AN:

736

East Asian (EAS)

AF:

0.996

AC:

1154

AN:

1159

South Asian (SAS)

AF:

0.663

AC:

893

AN:

1347

European-Finnish (FIN)

AF:

0.935

AC:

2748

AN:

2940

Middle Eastern (MID)

AF:

0.956

AC:

AN:

European-Non Finnish (NFE)

AF:

0.362

AC:

4730

AN:

13050

Other (OTH)

AF:

0.570

AC:

249

AN:

437

Age Distribution

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.450

Hom.:

27659

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.1

(source)

DANN

Benign

0.39

PhyloP100

-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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