NM_004681.4:c.16+1594C>T

Variant names:

• chrY-20577481-C-T
• rs9786153
• NM_004681.4:c.16+1594C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004681.4(EIF1AY):​c.16+1594C>T 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 0.66 (0 hom., 20847 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: EIF1AY NM_004681.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997
• Publications: 17 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF1AY	NM_004681.4	c.16+1594C>T		intron_variant	Intron 1 of 6	ENST00000361365.7	NP_004672.2
EIF1AY	NM_001278612.2	c.16+1594C>T		intron_variant	Intron 1 of 5		NP_001265541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF1AY	ENST00000361365.7	c.16+1594C>T		intron_variant	Intron 1 of 6	1	NM_004681.4	ENSP00000354722.2
EIF1AY	ENST00000382772.3	c.16+1594C>T		intron_variant	Intron 1 of 5	1		ENSP00000372222.3
EIF1AY	ENST00000465253.1	n.110+1594C>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.659 AC: 20788 AN: 31531 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.986

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.629

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.660 AC: 20847 AN: 31585 Hom.: 0 Cov.: 0 AF XY: 0.660 AC XY: 20847 AN XY: 31585

African (AFR) AF: 0.813 AC: 6513 AN: 8010

American (AMR) AF: 0.513 AC: 1784 AN: 3476

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 687 AN: 763

East Asian (EAS) AF: 0.999 AC: 1186 AN: 1187

South Asian (SAS) AF: 0.991 AC: 1366 AN: 1379

European-Finnish (FIN) AF: 0.971 AC: 2883 AN: 2968

Middle Eastern (MID) AF: 0.986 AC: 72 AN: 73

European-Non Finnish (NFE) AF: 0.460 AC: 6024 AN: 13091

Other (OTH) AF: 0.632 AC: 273 AN: 432

Alfa AF: 0.527 Hom.: 22325

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.6
DANN	Benign	0.23
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism

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: rs9786153; hg19: chrY-22739367;