rs3900

chrY-19568371-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_045128.1(TXLNGY):n.125+889G>C variant causes a intron, non coding transcript 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 0.43 (0 hom., 14199 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TXLNGY NR_045128.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

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.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Hemizygotes in GnomAd at 14145 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TXLNGY	NR_045128.1	n.125+889G>C		intron_variant, non_coding_transcript_variant
TXLNGY	NR_045129.1	n.125+889G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TXLNGY	ENST00000445715.6	n.101+889G>C		intron_variant, non_coding_transcript_variant
TXLNGY	ENST00000700762.1	n.195+801G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.431 AC: 14145 AN: 32811 Hom.: 0 Cov.: 0 AF XY: 0.431 AC XY: 14145 AN XY: 32811

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.443

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.432 AC: 14199 AN: 32874 Hom.: 0 Cov.: 0 AF XY: 0.432 AC XY: 14199 AN XY: 32874

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.442

Alfa AF: 0.350 Hom.: 4365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.69
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3900; hg19: chrY-21730257;