rs13447354

Positions:

• chrY-20589065-G-A

Variant summary

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

The NM_004681.4(EIF1AY):​c.338-419G>A 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 0.076 (0 hom., 2582 hem., cov: 0)
  • Exomes 𝑓: 0.072 (0 hom. 103 hem.)
• Consequence: EIF1AY NM_004681.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EIF1AY	NM_004681.4	c.338-419G>A		intron_variant		ENST00000361365.7
EIF1AY	NM_001278612.2	c.287-419G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIF1AY	ENST00000361365.7	c.338-419G>A		intron_variant		1	NM_004681.4	P1
EIF1AY	ENST00000382772.3	c.287-419G>A		intron_variant		1
EIF1AY	ENST00000464196.5	n.2348G>A		non_coding_transcript_exon_variant	1/2	2
EIF1AY	ENST00000485584.1	n.260-419G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 2584 AN: 34070 Hom.: 0 Cov.: 0 AF XY: 0.0758 AC XY: 2584 AN XY: 34070

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0250

Gnomad ASJ AF: 0.00257

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.000636

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0439

GnomAD4 exome AF: 0.0718 AC: 103 AN: 1435 Hom.: 0 Cov.: 0 AF XY: 0.0718 AC XY: 103 AN XY: 1435

Gnomad4 AFR exome AF: 0.0667

Gnomad4 AMR exome AF: 0.0142

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0606

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.182

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.0756 AC: 2582 AN: 34132 Hom.: 0 Cov.: 0 AF XY: 0.0756 AC XY: 2582 AN XY: 34132

Gnomad4 AFR AF: 0.0252

Gnomad4 AMR AF: 0.0247

Gnomad4 ASJ AF: 0.00257

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.000635

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.123 Hom.: 1740

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.24

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: rs13447354; hg19: chrY-22750951;