rs34742138

Positions:

• chrY-2978360-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003411.4(ZFY):​c.1222+280C>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 0.027 (0 hom., 886 hem., cov: 0)
• Consequence: ZFY NM_003411.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

Genes affected

ZFY (HGNC:12870): (zinc finger protein Y-linked) This gene encodes a zinc finger-containing protein that may function as a transcription factor. This gene was once a candidate gene for the testis-determining factor (TDF) and was erroneously referred to as TDF. [provided by RefSeq, Jul 2008]

ZFY-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFY	NM_003411.4	c.1222+280C>T		intron_variant		ENST00000155093.8	NP_003402.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFY	ENST00000155093.8	c.1222+280C>T		intron_variant		1	NM_003411.4	ENSP00000155093.3

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 883 AN: 32655 Hom.: 0 Cov.: 0 AF XY: 0.0270 AC XY: 883 AN XY: 32655

Gnomad AFR AF: 0.00548

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0803

Gnomad EAS AF: 0.000785

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.000628

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0370

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

GnomAD4 genome AF: 0.0271 AC: 886 AN: 32721 Hom.: 0 Cov.: 0 AF XY: 0.0271 AC XY: 886 AN XY: 32721

Gnomad4 AFR AF: 0.00545

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.0803

Gnomad4 EAS AF: 0.000786

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.000628

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0366

Alfa AF: 0.0404 Hom.: 1356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs34742138; hg19: chrY-2846401;