Variant Y-19004472-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000331787.2(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
ENST00000331787.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.917

Variant links:

Genes affected

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

TTTY14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
TTTY14	NR_001543.4 link	n.504-71631C>A	intron_variant
TTTY14	NR_125733.1 link	n.578+64252C>A	intron_variant
TTTY14	NR_125734.1 link	n.578+64252C>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
TTTY14	ENST00000331787.2 link	n.373-71631C>A	intron_variant	1
TTTY14	ENST00000452584.5 link	n.335+40070C>A	intron_variant	3
TTTY14	ENST00000454875.2 link	n.330+72573C>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

18284

AN:

31039

Hom.:

Cov.:

AF XY:

0.589

AC XY:

18284

AN XY:

31039

FAILED QC

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

Gnomad4 AFR

AF:

0.794

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.810

Gnomad4 EAS

AF:

0.997

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.932

Gnomad4 NFE

AF:

0.365

Gnomad4 OTH

AF:

0.571

Alfa

AF:

0.398

Hom.:

15353

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

DANN

Benign

0.18

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over