rs3900

Variant names:

• chrY-19568371-G-C
• rs3900
• ENST00000688167.3:n.1044G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000688167.3(TXLNGY):​n.1044G>C variant causes a non coding transcript exon 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 ENST00000688167.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 23 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=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688167.3. 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.125+889G>C		intron	N/A
	TXLNGY	NR_045129.1		n.125+889G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXLNGY	ENST00000688167.3		n.1044G>C		non_coding_transcript_exon	Exon 1 of 1
	TXLNGY	ENST00000407724.7	TSL:3	n.170+889G>C		intron	N/A
	TXLNGY	ENST00000445715.6	TSL:6	n.101+889G>C		intron	N/A

Frequencies

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

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

African (AFR) AF: 0.783 AC: 6480 AN: 8274

American (AMR) AF: 0.357 AC: 1308 AN: 3662

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 548 AN: 755

East Asian (EAS) AF: 0.128 AC: 164 AN: 1285

South Asian (SAS) AF: 0.392 AC: 581 AN: 1484

European-Finnish (FIN) AF: 0.154 AC: 508 AN: 3299

Middle Eastern (MID) AF: 0.904 AC: 66 AN: 73

European-Non Finnish (NFE) AF: 0.321 AC: 4286 AN: 13369

Other (OTH) AF: 0.442 AC: 205 AN: 464

Alfa AF: 0.350 Hom.: 4365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.24
PhyloP100		-1.9

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.

Other links and lift over

dbSNP: rs3900;

hg19: chrY-21730257;