Genetic Variant XGY2:n.106+14396C>T (chrY-2789135-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000679518.1(XGY2):n.106+14396C>T 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 0.062 ( 0 hom., 2134 hem., cov: 0)

Consequence

XGY2
ENST00000679518.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

15 publications found

Variant links:

Genes affected

XGY2 (HGNC:34022): (XG Y-linked 2 (pseudogene))

XGY2 links:

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new If you want to explore the variant's impact on the transcript ENST00000679518.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000679518.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
XGY2	ENST00000679518.1	n.106+14396C>T	intron	N/A
XGY2	ENST00000680285.1	n.320-614C>T	intron	N/A
XGY2	ENST00000681787.1	n.106+14396C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0620

AC:

2131

AN:

34370

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0187

Gnomad AMI

AF:

0.0188

Gnomad AMR

AF:

0.00702

Gnomad ASJ

AF:

0.0807

Gnomad EAS

AF:

0.00303

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.0364

Gnomad MID

AF:

0.0267

Gnomad NFE

AF:

0.0911

Gnomad OTH

AF:

0.0388

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

GnomAD4 genome

AF:

0.0620

AC:

2134

AN:

34433

Hom.:

Cov.:

AF XY:

0.0620

AC XY:

2134

AN XY:

34433

show subpopulations

African (AFR)

AF:

0.0190

AC:

170

AN:

8927

American (AMR)

AF:

0.00701

AC:

AN:

3854

Ashkenazi Jewish (ASJ)

AF:

0.0807

AC:

AN:

781

East Asian (EAS)

AF:

0.00303

AC:

AN:

1320

South Asian (SAS)

AF:

0.299

AC:

468

AN:

1567

European-Finnish (FIN)

AF:

0.0364

AC:

127

AN:

3485

Middle Eastern (MID)

AF:

0.0270

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0911

AC:

1250

AN:

13719

Other (OTH)

AF:

0.0385

AC:

AN:

493

Age Distribution

Genome Hom

Variant carriers

120

160

200

<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:

0.0933

Hom.:

4861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.2

(source)

DANN

Benign

0.38

PhyloP100

-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over