dbSNP rs13447352: EIF1AY:c.256-57A>C (chrY-20587967-A-C) – 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.256-57A>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 0.048 ( 0 hom., 1633 hem., cov: 0)

Exomes 𝑓: 0.070 ( 0 hom. 15034 hem. )

Consequence

EIF1AY
NM_004681.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720

Publications

15 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:

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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=-0.49).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004681.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF1AY	NM_004681.4	MANE Select	c.256-57A>C		intron	N/A	NP_004672.2
	EIF1AY	NM_001278612.2		c.205-57A>C		intron	N/A	NP_001265541.1	A6NJH9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EIF1AY	ENST00000361365.7	TSL:1 MANE Select	c.256-57A>C	intron	N/A	ENSP00000354722.2	O14602
EIF1AY	ENST00000382772.3	TSL:1	c.205-57A>C	intron	N/A	ENSP00000372222.3	A6NJH9
EIF1AY	ENST00000939723.1		c.250-57A>C	intron	N/A	ENSP00000609782.1

Frequencies

GnomAD3 genomes

AF:

0.0485

AC:

1633

AN:

33681

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0117

Gnomad AMI

AF:

0.0853

Gnomad AMR

AF:

0.0782

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.000775

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.000869

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.0479

Gnomad OTH

AF:

0.128

GnomAD4 exome

AF:

0.0699

AC:

15034

AN:

215039

Hom.:

Cov.:

AF XY:

0.0699

AC XY:

15034

AN XY:

215039

show subpopulations

African (AFR)

AF:

0.0171

AC:

AN:

4334

American (AMR)

AF:

0.105

AC:

731

AN:

6970

Ashkenazi Jewish (ASJ)

AF:

0.367

AC:

1977

AN:

5391

East Asian (EAS)

AF:

0.00101

AC:

AN:

7922

South Asian (SAS)

AF:

0.170

AC:

4380

AN:

25761

European-Finnish (FIN)

AF:

0.00169

AC:

AN:

11268

Middle Eastern (MID)

AF:

0.494

AC:

603

AN:

1220

European-Non Finnish (NFE)

AF:

0.0432

AC:

6177

AN:

142852

Other (OTH)

AF:

0.114

AC:

1065

AN:

9321

Age Distribution

Exome Hom

Variant carriers

160

320

480

640

800

<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:

0.0484

AC:

1633

AN:

33744

Hom.:

Cov.:

AF XY:

0.0484

AC XY:

1633

AN XY:

33744

show subpopulations

African (AFR)

AF:

0.0116

AC:

101

AN:

8720

American (AMR)

AF:

0.0781

AC:

286

AN:

3663

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

272

AN:

759

East Asian (EAS)

AF:

0.000775

AC:

AN:

1290

South Asian (SAS)

AF:

0.139

AC:

217

AN:

1557

European-Finnish (FIN)

AF:

0.000869

AC:

AN:

3451

Middle Eastern (MID)

AF:

0.348

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0480

AC:

651

AN:

13559

Other (OTH)

AF:

0.129

AC:

AN:

465

Age Distribution

Genome Hom

Variant carriers

120

150

<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:

0.103

Hom.:

1969

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

6.1

(source)

DANN

Benign

0.76

PhyloP100

-0.072

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over