chr5-41019840-A-G

Position:

• chr5-41019840-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173489.5(MROH2B):​c.2442-822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,218 control chromosomes in the GnomAD database, including 57,402 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.

• Frequency: Genomes: 𝑓 0.87 (57402 hom., cov: 33)
• Consequence: MROH2B NM_173489.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729

Genes affected

MROH2B (HGNC:26857): (maestro heat like repeat family member 2B) Predicted to be involved in protein kinase A signaling. Predicted to be located in acrosomal vesicle and sperm midpiece. [provided by Alliance of Genome Resources, Apr 2022]

MROH2B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MROH2B	NM_173489.5	c.2442-822T>C		intron_variant		ENST00000399564.5	NP_775760.3
MROH2B	XM_011513952.2	c.2442-822T>C		intron_variant			XP_011512254.1
MROH2B	XM_011513953.2	c.2256-822T>C		intron_variant			XP_011512255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MROH2B	ENST00000399564.5	c.2442-822T>C		intron_variant		1	NM_173489.5	ENSP00000382476.4

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131935 AN: 152100 Hom.: 57348 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.873

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.867 AC: 132049 AN: 152218 Hom.: 57402 Cov.: 33 AF XY: 0.866 AC XY: 64463 AN XY: 74422

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.873

Alfa AF: 0.858 Hom.: 20177

Bravo AF: 0.872

Asia WGS AF: 0.749 AC: 2605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.49

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

Other links and lift over

dbSNP: rs10058056; hg19: chr5-41019942;