Y-20588697-A-C

Variant names:

• chrY-20588697-A-C
• rs1558843
• NM_004681.4:c.337+592A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004681.4(EIF1AY):​c.337+592A>C 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 0.60 (0 hom., 19539 hem., cov: 0)
  • Exomes 𝑓: 0.33 (0 hom. 2 hem.)
  • Failed GnomAD Quality Control
• Consequence: EIF1AY NM_004681.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.79
• Publications: 5 publications found

Genes affected

EIF1AY (HGNC:3252): (eukaryotic translation initiation factor 1A Y-linked) This gene is located on the non-recombining region of the Y chromosome. It encodes a protein related to eukaryotic translation initiation factor 1A (EIF1A), which may function in stabilizing the binding of the initiator Met-tRNA to 40S ribosomal subunits. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004681.4. 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
	EIF1AY	NM_004681.4	MANE Select	c.337+592A>C		intron	N/A	NP_004672.2
	EIF1AY	NM_001278612.2		c.286+592A>C		intron	N/A	NP_001265541.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF1AY	ENST00000361365.7	TSL:1 MANE Select	c.337+592A>C		intron	N/A	ENSP00000354722.2
	EIF1AY	ENST00000382772.3	TSL:1	c.286+592A>C		intron	N/A	ENSP00000372222.3
	EIF1AY	ENST00000464196.5	TSL:2	n.1980A>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 19470 AN: 32752 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.564

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.595 AC: 19539 AN: 32812 Hom.: 0 Cov.: 0 AF XY: 0.595 AC XY: 19539 AN XY: 32812

African (AFR) AF: 0.795 AC: 6643 AN: 8361

American (AMR) AF: 0.499 AC: 1796 AN: 3601

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 619 AN: 761

East Asian (EAS) AF: 0.996 AC: 1249 AN: 1254

South Asian (SAS) AF: 0.655 AC: 978 AN: 1492

European-Finnish (FIN) AF: 0.932 AC: 2950 AN: 3165

Middle Eastern (MID) AF: 0.959 AC: 70 AN: 73

European-Non Finnish (NFE) AF: 0.366 AC: 4904 AN: 13416

Other (OTH) AF: 0.571 AC: 273 AN: 478

Alfa AF: 0.463 Hom.: 15724

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.40
PhyloP100		-3.8
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: rs1558843; hg19: chrY-22750583;