rs1558843

Positions:

• chrY-20588697-A-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EIF1AY	NM_004681.4	c.337+592A>C		intron_variant		ENST00000361365.7	NP_004672.2
EIF1AY	NM_001278612.2	c.286+592A>C		intron_variant			NP_001265541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EIF1AY	ENST00000361365.7	c.337+592A>C		intron_variant		1	NM_004681.4	ENSP00000354722.2
EIF1AY	ENST00000382772.3	c.286+592A>C		intron_variant		1		ENSP00000372222.3
EIF1AY	ENST00000464196.5	n.1980A>C		non_coding_transcript_exon_variant	1/2	2
EIF1AY	ENST00000485584.1	n.259+592A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 19470 AN: 32752 Hom.: 0 Cov.: 0 AF XY: 0.594 AC XY: 19470 AN XY: 32752 FAILED QC

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

Gnomad4 NFE exome AF: 0.333

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

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.571

Alfa AF: 0.397 Hom.: 8010

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.40

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: rs1558843; hg19: chrY-22750583;