rs13447352

chrY-20587967-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.256-57A>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 0.048 (0 hom., 1633 hem., cov: 0)
  • Exomes 𝑓: 0.070 (0 hom. 15034 hem.)
• Consequence: EIF1AY NM_004681.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

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=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EIF1AY	NM_004681.4	c.256-57A>C		intron_variant		ENST00000361365.7
EIF1AY	NM_001278612.2	c.205-57A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIF1AY	ENST00000361365.7	c.256-57A>C		intron_variant		1	NM_004681.4	P1

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 1633 AN: 33681 Hom.: 0 Cov.: 0 AF XY: 0.0485 AC XY: 1633 AN XY: 33681

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0853

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.000869

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.0699 AC: 15034 AN: 215039 Hom.: 0 Cov.: 0 AF XY: 0.0699 AC XY: 15034 AN XY: 215039

Gnomad4 AFR exome AF: 0.0171

Gnomad4 AMR exome AF: 0.105

Gnomad4 ASJ exome AF: 0.367

Gnomad4 EAS exome AF: 0.00101

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.00169

Gnomad4 NFE exome AF: 0.0432

Gnomad4 OTH exome AF: 0.114

GnomAD4 genome AF: 0.0484 AC: 1633 AN: 33744 Hom.: 0 Cov.: 0 AF XY: 0.0484 AC XY: 1633 AN XY: 33744

Gnomad4 AFR AF: 0.0116

Gnomad4 AMR AF: 0.0781

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.000869

Gnomad4 NFE AF: 0.0480

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0948 Hom.: 1407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	6.1
Dann	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs13447352; hg19: chrY-22749853;