dbSNP rs3908: TXLNGY:n.170+3797delG (chrY-19571278-CG-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000407724.7(TXLNGY):n.170+3797delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.058 ( 0 hom., 1937 hem., cov: 0)

Consequence

TXLNGY
ENST00000407724.7 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.415

Publications

11 publications found

Variant links:

Genes affected

TXLNGY (HGNC:):

TXLNGY links:

TXLNGY (HGNC:18473): (taxilin gamma Y-linked (pseudogene)) Predicted to enable syntaxin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

TXLNGY links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TXLNGY	NR_045128.1 link	n.125+3800delG		intron_variant	Intron 1 of 9
TXLNGY	NR_045129.1 link	n.125+3800delG		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TXLNGY	ENST00000407724.7 link	n.170+3797delG	intron_variant	Intron 1 of 4	3
TXLNGY	ENST00000445715.6 link	n.101+3797delG	intron_variant	Intron 1 of 9	6
TXLNGY	ENST00000447202.3 link	n.624+3328delG	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.0586

AC:

1938

AN:

33070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00995

Gnomad AMI

AF:

0.0231

Gnomad AMR

AF:

0.00599

Gnomad ASJ

AF:

0.0822

Gnomad EAS

AF:

0.00239

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.0334

Gnomad MID

AF:

0.0274

Gnomad NFE

AF:

0.0898

Gnomad OTH

AF:

0.0394

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

GnomAD4 genome

AF:

0.0585

AC:

1937

AN:

33131

Hom.:

Cov.:

AF XY:

0.0585

AC XY:

1937

AN XY:

33131

show subpopulations

African (AFR)

AF:

0.00989

AC:

AN:

8495

American (AMR)

AF:

0.00598

AC:

AN:

3682

Ashkenazi Jewish (ASJ)

AF:

0.0822

AC:

AN:

766

East Asian (EAS)

AF:

0.00239

AC:

AN:

1255

South Asian (SAS)

AF:

0.296

AC:

423

AN:

1427

European-Finnish (FIN)

AF:

0.0334

AC:

111

AN:

3327

Middle Eastern (MID)

AF:

0.0274

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0898

AC:

1206

AN:

13430

Other (OTH)

AF:

0.0391

AC:

AN:

460

Age Distribution

Genome Hom

Variant carriers

108

144

180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.41

Mutation Taster

=100/0

polymorphism

(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