dbSNP rs13447370: TXLNGY:n.4821+303C>T (chrY-19602614-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 ENST00000253320.8(TXLNGY):n.4821+303C>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 0.000031 ( 0 hom., 1 hem., cov: 0)

Consequence

TXLNGY
ENST00000253320.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20

Publications

4 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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000253320.8, 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: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000253320.8. 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
	TXLNGY	NR_045128.1		n.1274+303C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
TXLNGY	ENST00000253320.8	TSL:2	n.4821+303C>T	intron	N/A
TXLNGY	ENST00000445715.6	TSL:6	n.1250+303C>T	intron	N/A
TXLNGY	ENST00000592697.1	TSL:3	n.586+303C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000308

AC:

AN:

32498

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000284

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.0000308

AC:

AN:

32498

Hom.:

Cov.:

AF XY:

0.0000308

AC XY:

AN XY:

32498

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

8331

American (AMR)

AF:

0.000284

AC:

AN:

3515

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

760

East Asian (EAS)

AF:

0.00

AC:

AN:

1245

South Asian (SAS)

AF:

0.00

AC:

AN:

1428

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3289

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

13188

Other (OTH)

AF:

0.00

AC:

AN:

456

Alfa

AF:

0.00770

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

2.1

(source)

DANN

Benign

0.41

PhyloP100

-2.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over