Variant rs4750568 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080836.3(MEIG1):c.26A>C(p.Lys9Thr) variant causes a missense change. The variant allele was found at a frequency of 0.669 in 1,607,570 control chromosomes in the GnomAD database, including 362,486 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.64 ( 31583 hom., cov: 31)

Exomes 𝑓: 0.67 ( 330903 hom. )

Consequence

MEIG1
NM_001080836.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.87

Variant links:

Genes affected

MEIG1 (HGNC:23429): (meiosis/spermiogenesis associated 1) Predicted to act upstream of or within cellular protein localization; manchette assembly; and sperm axoneme assembly. Predicted to be located in cytosol and manchette. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MEIG1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.392923E-6).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MEIG1	NM_001080836.3 linkuse as main transcript	c.26A>C	p.Lys9Thr	missense_variant	2/3	ENST00000407572.6	NP_001074305.1
MEIG1	XM_024448136.1 linkuse as main transcript	c.119A>C	p.Lys40Thr	missense_variant	2/3		XP_024303904.1
MEIG1	XM_047425662.1 linkuse as main transcript	c.26A>C	p.Lys9Thr	missense_variant	2/3		XP_047281618.1
MEIG1	NR_147060.2 linkuse as main transcript	n.170+6937A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
MEIG1	ENST00000407572.6 linkuse as main transcript	c.26A>C	p.Lys9Thr	missense_variant	2/3	2	NM_001080836.3	ENSP00000384334	P1
MEIG1	ENST00000378240.1 linkuse as main transcript	c.26A>C	p.Lys9Thr	missense_variant	1/2	2		ENSP00000367486	P1
MEIG1	ENST00000477770.5 linkuse as main transcript	n.120-6019A>C		intron_variant, non_coding_transcript_variant		2
MEIG1	ENST00000496225.2 linkuse as main transcript	n.49-3754A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97440

AN:

151854

Hom.:

31577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.579

Gnomad AMI

AF:

0.669

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.627

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.685

Gnomad OTH

AF:

0.641

GnomAD3 exomes

AF:

0.657

AC:

162190

AN:

247050

Hom.:

53842

AF XY:

0.658

AC XY:

87831

AN XY:

133484

show subpopulations

Gnomad AFR exome

AF:

0.573

Gnomad AMR exome

AF:

0.723

Gnomad ASJ exome

AF:

0.610

Gnomad EAS exome

AF:

0.479

Gnomad SAS exome

AF:

0.674

Gnomad FIN exome

AF:

0.630

Gnomad NFE exome

AF:

0.682

Gnomad OTH exome

AF:

0.657

GnomAD4 exome

AF:

0.672

AC:

978378

AN:

1455598

Hom.:

330903

Cov.:

AF XY:

0.672

AC XY:

486273

AN XY:

724044

show subpopulations

Gnomad4 AFR exome

AF:

0.573

Gnomad4 AMR exome

AF:

0.718

Gnomad4 ASJ exome

AF:

0.608

Gnomad4 EAS exome

AF:

0.451

Gnomad4 SAS exome

AF:

0.669

Gnomad4 FIN exome

AF:

0.630

Gnomad4 NFE exome

AF:

0.685

Gnomad4 OTH exome

AF:

0.666

GnomAD4 genome

AF:

0.642

AC:

97495

AN:

151972

Hom.:

31583

Cov.:

AF XY:

0.640

AC XY:

47546

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.579

Gnomad4 AMR

AF:

0.685

Gnomad4 ASJ

AF:

0.602

Gnomad4 EAS

AF:

0.471

Gnomad4 SAS

AF:

0.670

Gnomad4 FIN

AF:

0.627

Gnomad4 NFE

AF:

0.685

Gnomad4 OTH

AF:

0.643

Alfa

AF:

0.669

Hom.:

75492

Bravo

AF:

0.643

TwinsUK

AF:

0.680

AC:

2520

ALSPAC

AF:

0.685

AC:

2640

ESP6500AA

AF:

0.585

AC:

2577

ESP6500EA

AF:

0.688

AC:

5918

ExAC

AF:

0.659

AC:

80011

Asia WGS

AF:

0.615

AC:

2142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.44

T;T

Eigen

Uncertain

0.49

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Uncertain

0.93

LIST_S2

Benign

0.78

T;.

MetaRNN

Benign

0.0000084

T;T

MetaSVM

Benign

-0.97

MutationTaster

Benign

0.00026

P;P

PrimateAI

Uncertain

0.50

PROVEAN

Uncertain

-2.9

D;D

REVEL

Benign

0.19

Sift

Benign

0.30

T;T

Sift4G

Benign

0.29

T;T

Polyphen

0.99

D;D

Vest4

0.21

MPC

0.054

ClinPred

0.038

GERP RS

5.7

Varity_R

0.54

gMVP

0.52

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over