rs373035025

Variant names:

• chr16-1844951-G-A
• NM_001163560.3:c.791C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-1844951-G-A
• chr16-1844951-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001163560.3(MEIOB):​c.791C>T​(p.Ala264Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000074 in 1,350,900 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.4e-7 (0 hom.)
• Consequence: MEIOB NM_001163560.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.98

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEIOB	NM_001163560.3	c.791C>T	p.Ala264Val	missense_variant	Exon 10 of 14	ENST00000325962.9	NP_001157032.1
MEIOB	NM_152764.3	c.791C>T	p.Ala264Val	missense_variant	Exon 10 of 13		NP_689977.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEIOB	ENST00000325962.9	c.791C>T	p.Ala264Val	missense_variant	Exon 10 of 14	5	NM_001163560.3	ENSP00000314484.3
MEIOB	ENST00000397344.7	c.791C>T	p.Ala264Val	missense_variant	Exon 10 of 13	5		ENSP00000380504.3
ENSG00000289722	ENST00000470044.5	c.170C>T	p.Ala57Val	missense_variant	Exon 9 of 13	2		ENSP00000457416.1
MEIOB	ENST00000496541.6	c.*9C>T		downstream_gene_variant		5		ENSP00000456880.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.40e-7 AC: 1 AN: 1350900 Hom.: 0 Cov.: 20 AF XY: 0.00000148 AC XY: 1 AN XY: 673910

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.79e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.070
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.22	T;.;T
Eigen	Pathogenic	0.79
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.86	D;D;D
M_CAP	Benign	0.012	T
MetaRNN	Uncertain	0.72	D;D;D
MetaSVM	Benign	-0.69	T
MutationAssessor	Uncertain	2.7	.;M;M
PrimateAI	Uncertain	0.52	T
PROVEAN	Uncertain	-2.9	D;D;D
REVEL	Uncertain	0.32
Sift	Uncertain	0.0050	D;D;D
Sift4G	Uncertain	0.0050	D;D;D
Polyphen		1.0	.;.;D
Vest4		0.68
MutPred		0.54		.;Loss of helix (P = 0.0167);Loss of helix (P = 0.0167);
MVP		0.23
ClinPred		0.96	D
GERP RS		6.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.38
gMVP		0.89

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-1894952;