rs17323322

Variant names:

• chrY-20584900-T-C
• rs17323322
• NM_004681.4:c.255+376T>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.255+376T>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 0.0056 (0 hom., 188 hem., cov: 0)
• Consequence: EIF1AY NM_004681.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF1AY	NM_004681.4	c.255+376T>C		intron_variant	Intron 4 of 6	ENST00000361365.7	NP_004672.2
EIF1AY	NM_001278612.2	c.204+2207T>C		intron_variant	Intron 3 of 5		NP_001265541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF1AY	ENST00000361365.7	c.255+376T>C		intron_variant	Intron 4 of 6	1	NM_004681.4	ENSP00000354722.2
EIF1AY	ENST00000382772.3	c.204+2207T>C		intron_variant	Intron 3 of 5	1		ENSP00000372222.3
EIF1AY	ENST00000465253.1	n.349+376T>C		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.00562 AC: 188 AN: 33446 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.00130

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00212

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

GnomAD4 genome AF: 0.00561 AC: 188 AN: 33505 Hom.: 0 Cov.: 0 AF XY: 0.00561 AC XY: 188 AN XY: 33505

African (AFR) AF: 0.00 AC: 0 AN: 8634

American (AMR) AF: 0.00 AC: 0 AN: 3600

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 770

East Asian (EAS) AF: 0.143 AC: 185 AN: 1291

South Asian (SAS) AF: 0.00130 AC: 2 AN: 1537

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3362

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 13549

Other (OTH) AF: 0.00211 AC: 1 AN: 474

Alfa AF: 0.00802 Hom.: 60

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.2
DANN	Benign	0.26
PhyloP100		-1.7

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: rs17323322; hg19: chrY-22746786;