Variant 7-39572602-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_020192.5(YAE1):c.577C>T(p.His193Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00348 in 1,614,054 control chromosomes in the GnomAD database, including 138 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 81 hom., cov: 32)

Exomes 𝑓: 0.0021 ( 57 hom. )

Consequence

YAE1
NM_020192.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.403

Variant links:

Genes affected

YAE1 (HGNC:24857): (YAE1 maturation factor of ABCE1) Involved in protein maturation by [4Fe-4S] cluster transfer. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

YAE1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00203982).

BP6

Variant 7-39572602-C-T is Benign according to our data. Variant chr7-39572602-C-T is described in ClinVar as [Benign]. Clinvar id is 778301.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YAE1	NM_020192.5 linkuse as main transcript	c.577C>T	p.His193Tyr	missense_variant	3/3	ENST00000223273.7
YAE1	NM_001282446.2 linkuse as main transcript	c.251+1975C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YAE1	ENST00000223273.7 linkuse as main transcript	c.577C>T	p.His193Tyr	missense_variant	3/3	1	NM_020192.5	P1	Q9NRH1-1
YAE1	ENST00000432096.2 linkuse as main transcript	c.251+1975C>T		intron_variant		2			Q9NRH1-2
YAE1	ENST00000485025.1 linkuse as main transcript			downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0165

AC:

2512

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0562

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00622

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000515

Gnomad OTH

AF:

0.0139

GnomAD3 exomes

AF:

0.00481

AC:

1209

AN:

251314

Hom.:

AF XY:

0.00358

AC XY:

486

AN XY:

135822

show subpopulations

Gnomad AFR exome

AF:

0.0578

Gnomad AMR exome

AF:

0.00408

Gnomad ASJ exome

AF:

0.00447

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.000554

Gnomad OTH exome

AF:

0.00294

GnomAD4 exome

AF:

0.00212

AC:

3098

AN:

1461772

Hom.:

Cov.:

AF XY:

0.00180

AC XY:

1310

AN XY:

727188

show subpopulations

Gnomad4 AFR exome

AF:

0.0580

Gnomad4 AMR exome

AF:

0.00458

Gnomad4 ASJ exome

AF:

0.00482

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000812

Gnomad4 FIN exome

AF:

0.0000936

Gnomad4 NFE exome

AF:

0.000485

Gnomad4 OTH exome

AF:

0.00431

GnomAD4 genome

AF:

0.0165

AC:

2519

AN:

152282

Hom.:

Cov.:

AF XY:

0.0163

AC XY:

1212

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0562

Gnomad4 AMR

AF:

0.00621

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000515

Gnomad4 OTH

AF:

0.0137

Alfa

AF:

0.00322

Hom.:

Bravo

AF:

0.0190

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.0515

AC:

227

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.00576

AC:

699

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.000654

EpiControl

AF:

0.000652

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

May 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.70

Cadd

Benign

Dann

Benign

0.53

DEOGEN2

Benign

0.0050

Eigen

Benign

-0.74

Eigen_PC

Benign

-0.68

FATHMM_MKL

Benign

0.093

LIST_S2

Benign

0.58

MetaRNN

Benign

0.0020

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.89

REVEL

Benign

0.12

Sift

Benign

0.65

Sift4G

Benign

1.0

Polyphen

0.019

Vest4

0.12

MVP

0.076

MPC

0.16

ClinPred

0.011

GERP RS

3.1

Varity_R

0.039

gMVP

0.11

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over