rs3908

chrY-19571278-CG-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_045128.1(TXLNGY):n.125+3800del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0585 in 33,131 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 NR_045128.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TXLNGY	NR_045128.1	n.125+3800del		intron_variant, non_coding_transcript_variant
TXLNGY	NR_045129.1	n.125+3800del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TXLNGY	ENST00000445715.6	n.101+3800del		intron_variant, non_coding_transcript_variant
TXLNGY	ENST00000700762.1	n.195+3712del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 1938 AN: 33070 Hom.: 0 Cov.: 0 AF XY: 0.0586 AC XY: 1938 AN XY: 33070

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.: 0 Cov.: 0 AF XY: 0.0585 AC XY: 1937 AN XY: 33131

Gnomad4 AFR AF: 0.00989

Gnomad4 AMR AF: 0.00598

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.00239

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.0334

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.0391

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3908; hg19: chrY-21733164;