rs13447370

Variant names:

• chrY-19602614-C-T
• rs13447370
• ENST00000253320.8:n.4821+303C>T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 4 publications found

Genes affected

TXLNGY (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TXLNGY	NR_045128.1	n.1274+303C>T		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TXLNGY	ENST00000253320.8	n.4821+303C>T		intron_variant	Intron 4 of 4	2
TXLNGY	ENST00000445715.6	n.1250+303C>T		intron_variant	Intron 9 of 9	6
TXLNGY	ENST00000592697.1	n.586+303C>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0000308 AC: 1 AN: 32498 Hom.: 0 Cov.: 0

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: 1 AN: 32498 Hom.: 0 Cov.: 0 AF XY: 0.0000308 AC XY: 1 AN XY: 32498

African (AFR) AF: 0.00 AC: 0 AN: 8331

American (AMR) AF: 0.000284 AC: 1 AN: 3515

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 760

East Asian (EAS) AF: 0.00 AC: 0 AN: 1245

South Asian (SAS) AF: 0.00 AC: 0 AN: 1428

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3289

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 13188

Other (OTH) AF: 0.00 AC: 0 AN: 456

Alfa AF: 0.00770 Hom.: 14

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs13447370; hg19: chrY-21764500;