NM_003411.4:c.1222+280C>T

Variant names:

• chrY-2978360-C-T
• rs34742138
• NM_003411.4:c.1222+280C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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:38798): (ZFY antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003411.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFY	NM_003411.4	MANE Select	c.1222+280C>T		intron	N/A	NP_003402.2
	ZFY	NM_001369702.1		c.1222+280C>T		intron	N/A	NP_001356631.1
	ZFY	NM_001369703.1		c.1144+280C>T		intron	N/A	NP_001356632.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFY	ENST00000155093.8	TSL:1 MANE Select	c.1222+280C>T		intron	N/A	ENSP00000155093.3
	ZFY	ENST00000449237.4	TSL:1	c.991+280C>T		intron	N/A	ENSP00000393908.1
	ZFY	ENST00000383052.5	TSL:5	c.1222+280C>T		intron	N/A	ENSP00000372525.1

Frequencies

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

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

African (AFR) AF: 0.00545 AC: 46 AN: 8446

American (AMR) AF: 0.0580 AC: 208 AN: 3584

Ashkenazi Jewish (ASJ) AF: 0.0803 AC: 62 AN: 772

East Asian (EAS) AF: 0.000786 AC: 1 AN: 1273

South Asian (SAS) AF: 0.0387 AC: 56 AN: 1448

European-Finnish (FIN) AF: 0.000628 AC: 2 AN: 3184

Middle Eastern (MID) AF: 0.203 AC: 14 AN: 69

European-Non Finnish (NFE) AF: 0.0339 AC: 450 AN: 13266

Other (OTH) AF: 0.0366 AC: 17 AN: 464

Alfa AF: 0.0497 Hom.: 2401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.43
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs34742138; hg19: chrY-2846401;