dbSNP rs9786232: TTTY14:n.373-71631C>A (chrY-19004472-G-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.373-71631C>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., 18350 hem., cov: 0)

Failed GnomAD Quality Control

Consequence

TTTY14
ENST00000331787.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.917

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=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TTTY14	NR_001543.4 link	n.504-71631C>A	intron_variant	Intron 1 of 1
TTTY14	NR_125733.1 link	n.578+64252C>A	intron_variant	Intron 2 of 4
TTTY14	NR_125734.1 link	n.578+64252C>A	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TTTY14	ENST00000331787.3 link	n.373-71631C>A	intron_variant	Intron 1 of 1	1
TTTY14	ENST00000452584.5 link	n.335+40070C>A	intron_variant	Intron 4 of 4	3
TTTY14	ENST00000454875.3 link	n.448+72573C>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

18284

AN:

31039

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.792

Gnomad AMI

AF:

0.263

Gnomad AMR

AF:

0.496

Gnomad ASJ

AF:

0.810

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.932

Gnomad MID

AF:

0.972

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.564

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:

0.590

AC:

18350

AN:

31096

Hom.:

Cov.:

AF XY:

0.590

AC XY:

18350

AN XY:

31096

show subpopulations

African (AFR)

AF:

0.794

AC:

6181

AN:

7786

American (AMR)

AF:

0.497

AC:

1669

AN:

3358

Ashkenazi Jewish (ASJ)

AF:

0.810

AC:

595

AN:

735

East Asian (EAS)

AF:

0.997

AC:

1162

AN:

1166

South Asian (SAS)

AF:

0.649

AC:

867

AN:

1335

European-Finnish (FIN)

AF:

0.932

AC:

2735

AN:

2933

Middle Eastern (MID)

AF:

0.972

AC:

AN:

European-Non Finnish (NFE)

AF:

0.365

AC:

4770

AN:

13073

Other (OTH)

AF:

0.571

AC:

248

AN:

434

Age Distribution

Genome Hom

Variant carriers

246

492

738

984

1230

<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:

0.441

Hom.:

23357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.23

(source)

DANN

Benign

0.18

PhyloP100

-0.92

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