Variant chr17-44667812-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001145080.3(MEIOC):c.1901A>G(p.Tyr634Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0132 in 1,613,878 control chromosomes in the GnomAD database, including 355 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.014 ( 61 hom., cov: 32)

Exomes 𝑓: 0.013 ( 294 hom. )

Consequence

MEIOC
NM_001145080.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.51

Variant links:

Genes affected

MEIOC (HGNC:26670): (meiosis specific with coiled-coil domain) Predicted to be involved in several processes, including gamete generation; germline cell cycle switching, mitotic to meiotic cell cycle; and mRNA stabilization. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MEIOC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0048514307).

BP6

Variant 17-44667812-A-G is Benign according to our data. Variant chr17-44667812-A-G is described in ClinVar as [Benign]. Clinvar id is 3387873.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 61 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEIOC	NM_001145080.3 linkuse as main transcript	c.1901A>G	p.Tyr634Cys	missense_variant	5/8	ENST00000409122.7	NP_001138552.2	A2RUB1-4
MEIOC	XM_005257236.4 linkuse as main transcript	c.1901A>G	p.Tyr634Cys	missense_variant	5/9		XP_005257293.1
MEIOC	XM_047435802.1 linkuse as main transcript	c.1901A>G	p.Tyr634Cys	missense_variant	5/6		XP_047291758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEIOC	ENST00000409122.7 linkuse as main transcript	c.1901A>G	p.Tyr634Cys	missense_variant	5/8	5	NM_001145080.3	ENSP00000386452.1		A2RUB1-4
MEIOC	ENST00000409464.1 linkuse as main transcript	c.1403A>G	p.Tyr468Cys	missense_variant	2/3	2		ENSP00000386586.1		A2RUB1-1

Frequencies

GnomAD3 genomes

AF:

0.0139

AC:

2112

AN:

152236

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.00890

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00248

Gnomad FIN

AF:

0.0789

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0149

Gnomad OTH

AF:

0.00861

GnomAD3 exomes

AF:

0.0151

AC:

3788

AN:

250700

Hom.:

AF XY:

0.0150

AC XY:

2027

AN XY:

135496

show subpopulations

Gnomad AFR exome

AF:

0.00154

Gnomad AMR exome

AF:

0.00388

Gnomad ASJ exome

AF:

0.00169

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00265

Gnomad FIN exome

AF:

0.0768

Gnomad NFE exome

AF:

0.0157

Gnomad OTH exome

AF:

0.0157

GnomAD4 exome

AF:

0.0132

AC:

19261

AN:

1461524

Hom.:

294

Cov.:

AF XY:

0.0128

AC XY:

9315

AN XY:

727026

show subpopulations

Gnomad4 AFR exome

AF:

0.00134

Gnomad4 AMR exome

AF:

0.00360

Gnomad4 ASJ exome

AF:

0.00188

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00304

Gnomad4 FIN exome

AF:

0.0772

Gnomad4 NFE exome

AF:

0.0125

Gnomad4 OTH exome

AF:

0.0124

GnomAD4 genome

AF:

0.0139

AC:

2113

AN:

152354

Hom.:

Cov.:

AF XY:

0.0165

AC XY:

1227

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00889

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00269

Gnomad4 FIN

AF:

0.0789

Gnomad4 NFE

AF:

0.0149

Gnomad4 OTH

AF:

0.00852

Alfa

AF:

0.0124

Hom.:

Bravo

AF:

0.00747

TwinsUK

AF:

0.0121

AC:

ALSPAC

AF:

0.0122

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0129

AC:

111

ExAC

AF:

0.0153

AC:

1859

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.00981

EpiControl

AF:

0.0113

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

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2024

MEIOC: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.32

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.076

T;.

Eigen

Uncertain

0.63

Eigen_PC

Uncertain

0.64

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.84

T;D

MetaRNN

Benign

0.0049

T;T

MetaSVM

Benign

-0.90

PROVEAN

Uncertain

-3.2

D;D

REVEL

Benign

0.26

Sift

Uncertain

0.0030

D;D

Sift4G

Benign

0.099

T;D

Polyphen

1.0

D;D

Vest4

0.63

MPC

0.35

ClinPred

0.025

GERP RS

5.7

Varity_R

0.17

gMVP

0.42

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