rs13447378

Variant names:

• chrY-20579854-G-C
• rs13447378
• NM_004681.4:c.100+163G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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 -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 rank	MANE	Protein	UniProt
EIF1AY	NM_004681.4	c.100+163G>C		intron_variant	Intron 2 of 6	ENST00000361365.7	NP_004672.2
EIF1AY	NM_001278612.2	c.100+163G>C		intron_variant	Intron 2 of 5		NP_001265541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF1AY	ENST00000361365.7	c.100+163G>C		intron_variant	Intron 2 of 6	1	NM_004681.4	ENSP00000354722.2
EIF1AY	ENST00000382772.3	c.100+163G>C		intron_variant	Intron 2 of 5	1		ENSP00000372222.3
EIF1AY	ENST00000465253.1	n.194+163G>C		intron_variant	Intron 2 of 4	2

Frequencies

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

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

African (AFR) AF: 0.000359 AC: 3 AN: 8360

American (AMR) AF: 0.000566 AC: 2 AN: 3532

Ashkenazi Jewish (ASJ) AF: 0.00931 AC: 7 AN: 752

East Asian (EAS) AF: 0.00 AC: 0 AN: 1284

South Asian (SAS) AF: 0.00664 AC: 10 AN: 1505

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3231

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.00119 AC: 16 AN: 13430

Other (OTH) AF: 0.00438 AC: 2 AN: 457

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
PhyloP100		-0.098
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs13447378; hg19: chrY-22741740;