dbSNP rs13447354: EIF1AY:c.338-419G>A (chrY-20589065-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004681.4(EIF1AY):c.338-419G>A 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 0.076 ( 0 hom., 2582 hem., cov: 0)

Exomes 𝑓: 0.072 ( 0 hom. 103 hem. )

Consequence

EIF1AY
NM_004681.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.222

Publications

5 publications found

Variant links:

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]

EIF1AY links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF1AY	NM_004681.4 link	c.338-419G>A		intron_variant	Intron 5 of 6	ENST00000361365.7	NP_004672.2	O14602
EIF1AY	NM_001278612.2 link	c.287-419G>A		intron_variant	Intron 4 of 5		NP_001265541.1	O14602A6NJH9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
EIF1AY	ENST00000361365.7 link	c.338-419G>A	intron_variant	Intron 5 of 6	1	NM_004681.4	ENSP00000354722.2	O14602
EIF1AY	ENST00000382772.3 link	c.287-419G>A	intron_variant	Intron 4 of 5	1		ENSP00000372222.3	A6NJH9
EIF1AY	ENST00000464196.5 link	n.2348G>A	non_coding_transcript_exon_variant	Exon 1 of 2	2
EIF1AY	ENST00000485584.1 link	n.260-419G>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0758

AC:

2584

AN:

34070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0254

Gnomad AMI

AF:

0.0330

Gnomad AMR

AF:

0.0250

Gnomad ASJ

AF:

0.00257

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.000636

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.0439

GnomAD4 exome

AF:

0.0718

AC:

103

AN:

1435

Hom.:

Cov.:

AF XY:

0.0718

AC XY:

103

AN XY:

1435

show subpopulations

African (AFR)

AF:

0.0667

AC:

AN:

American (AMR)

AF:

0.0142

AC:

AN:

212

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.0606

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

334

European-Finnish (FIN)

AF:

0.182

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.116

AC:

AN:

731

Other (OTH)

AF:

0.125

AC:

AN:

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0756

AC:

2582

AN:

34132

Hom.:

Cov.:

AF XY:

0.0756

AC XY:

2582

AN XY:

34132

show subpopulations

African (AFR)

AF:

0.0252

AC:

223

AN:

8832

American (AMR)

AF:

0.0247

AC:

AN:

3768

Ashkenazi Jewish (ASJ)

AF:

0.00257

AC:

AN:

777

East Asian (EAS)

AF:

0.103

AC:

134

AN:

1295

South Asian (SAS)

AF:

0.000635

AC:

AN:

1575

European-Finnish (FIN)

AF:

0.152

AC:

523

AN:

3442

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.115

AC:

1578

AN:

13675

Other (OTH)

AF:

0.0436

AC:

AN:

482

Age Distribution

Genome Hom

Variant carriers

102

136

170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.129

Hom.:

2419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.8

(source)

DANN

Benign

0.24

PhyloP100

-0.22

Mutation Taster

=100/0

polymorphism

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over