rs13447378

Positions:

• chrY-20579854-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_004681.4(EIF1AY):​c.100+163G>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 0.0012 (0 hom., 40 hem., cov: 0)
• Consequence: EIF1AY NM_004681.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Hemizygotes in GnomAd4 at 40 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EIF1AY	NM_004681.4	c.100+163G>C		intron_variant		ENST00000361365.7	NP_004672.2
EIF1AY	NM_001278612.2	c.100+163G>C		intron_variant			NP_001265541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EIF1AY	ENST00000361365.7	c.100+163G>C		intron_variant		1	NM_004681.4	ENSP00000354722	P1
EIF1AY	ENST00000382772.3	c.100+163G>C		intron_variant		1		ENSP00000372222
EIF1AY	ENST00000465253.1	n.194+163G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00122 AC: 40 AN: 32776 Hom.: 0 Cov.: 0 AF XY: 0.00122 AC XY: 40 AN XY: 32776

Gnomad AFR AF: 0.000361

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000567

Gnomad ASJ AF: 0.00931

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00667

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00119

Gnomad OTH AF: 0.00441

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00122 AC: 40 AN: 32840 Hom.: 0 Cov.: 0 AF XY: 0.00122 AC XY: 40 AN XY: 32840

Gnomad4 AFR AF: 0.000359

Gnomad4 AMR AF: 0.000566

Gnomad4 ASJ AF: 0.00931

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00664

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00119

Gnomad4 OTH AF: 0.00438

Alfa AF: 0.00128 Hom.: 18

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs13447378; hg19: chrY-22741740;