Genetic Variant MEIOB:p.Thr277Thr (chr16-1844911-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001163560.3(MEIOB):c.831G>A(p.Thr277Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 1,526,526 control chromosomes in the GnomAD database, including 72,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.33 ( 8207 hom., cov: 32)

Exomes 𝑓: 0.30 ( 64100 hom. )

Consequence

MEIOB
NM_001163560.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.158

Variant links:

Genes affected

MEIOB (HGNC:28569): (meiosis specific with OB-fold) Predicted to enable chromatin binding activity; single-stranded DNA 3'-5' exodeoxyribonuclease activity; and single-stranded DNA binding activity. Predicted to be involved in double-strand break repair via homologous recombination; fertilization; and meiotic nuclear division. Predicted to be located in cytoplasm. Implicated in spermatogenic failure 22. [provided by Alliance of Genome Resources, Apr 2022]

MEIOB 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 (BayesDel_noAF=-0.77).

BP6

Variant 16-1844911-C-T is Benign according to our data. Variant chr16-1844911-C-T is described in ClinVar as [Benign]. Clinvar id is 3060040.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.158 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEIOB	NM_001163560.3 link	c.831G>A	p.Thr277Thr	synonymous_variant	Exon 10 of 14	ENST00000325962.9	NP_001157032.1	Q8N635-2
MEIOB	NM_152764.3 link	c.831G>A	p.Thr277Thr	synonymous_variant	Exon 10 of 13		NP_689977.2	Q8N635-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
MEIOB	ENST00000325962.9 link	c.831G>A	p.Thr277Thr	synonymous_variant	Exon 10 of 14	5	NM_001163560.3	ENSP00000314484.3	Q8N635-2
MEIOB	ENST00000397344.7 link	c.831G>A	p.Thr277Thr	synonymous_variant	Exon 10 of 13	5		ENSP00000380504.3	Q8N635-1
ENSG00000289722	ENST00000470044.5 link	c.210G>A	p.Thr70Thr	synonymous_variant	Exon 9 of 13	2		ENSP00000457416.1	H3BU10
MEIOB	ENST00000496541.6 link	c.*49G>A		downstream_gene_variant		5		ENSP00000456880.1	H3BSU6

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49467

AN:

151844

Hom.:

8207

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.420

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.302

GnomAD3 exomes

AF:

0.322

AC:

77564

AN:

241088

Hom.:

13105

AF XY:

0.327

AC XY:

42541

AN XY:

130188

show subpopulations

Gnomad AFR exome

AF:

0.332

Gnomad AMR exome

AF:

0.247

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.420

Gnomad SAS exome

AF:

0.418

Gnomad FIN exome

AF:

0.398

Gnomad NFE exome

AF:

0.292

Gnomad OTH exome

AF:

0.316

GnomAD4 exome

AF:

0.296

AC:

407043

AN:

1374564

Hom.:

64100

Cov.:

AF XY:

0.301

AC XY:

206483

AN XY:

684890

show subpopulations

Gnomad4 AFR exome

AF:

0.319

Gnomad4 AMR exome

AF:

0.259

Gnomad4 ASJ exome

AF:

0.270

Gnomad4 EAS exome

AF:

0.477

Gnomad4 SAS exome

AF:

0.416

Gnomad4 FIN exome

AF:

0.393

Gnomad4 NFE exome

AF:

0.276

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.326

AC:

49494

AN:

151962

Hom.:

8207

Cov.:

AF XY:

0.334

AC XY:

24771

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.335

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.270

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.420

Gnomad4 FIN

AF:

0.408

Gnomad4 NFE

AF:

0.298

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.299

Hom.:

8618

Bravo

AF:

0.313

Asia WGS

AF:

0.414

AC:

1438

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MEIOB-related disorder

Benign:1

Oct 22, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.4

DANN

Benign

0.67

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