5-41033829-C-CTATCTTATT

Position:

• chr5-41033829-C-CTATCTTATT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000399564.5(MROH2B):​c.2241+8_2241+9insAATAAGATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 1,324,924 control chromosomes in the GnomAD database, including 54 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0038 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0025 (52 hom.)
• Consequence: MROH2B ENST00000399564.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MROH2B	NM_173489.5	c.2241+8_2241+9insAATAAGATA		intron_variant		ENST00000399564.5	NP_775760.3
MROH2B	XM_011513952.2	c.2241+8_2241+9insAATAAGATA		intron_variant			XP_011512254.1
MROH2B	XM_011513953.2	c.2055+8_2055+9insAATAAGATA		intron_variant			XP_011512255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MROH2B	ENST00000399564.5	c.2241+8_2241+9insAATAAGATA		intron_variant		1	NM_173489.5	ENSP00000382476	P1
MROH2B	ENST00000506092.6	c.906+8_906+9insAATAAGATA		intron_variant		2		ENSP00000441504
MROH2B	ENST00000503890.5	n.1203+8_1203+9insAATAAGATA		intron_variant, non_coding_transcript_variant		2
MROH2B	ENST00000515297.5	n.1629+8_1629+9insAATAAGATA		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00379 AC: 553 AN: 146062 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.000876

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0116

Gnomad ASJ AF: 0.00330

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00459

Gnomad FIN AF: 0.00109

Gnomad MID AF: 0.00329

Gnomad NFE AF: 0.00434

Gnomad OTH AF: 0.00855

GnomAD3 exomes AF: 0.00330 AC: 437 AN: 132376 Hom.: 8 AF XY: 0.00321 AC XY: 226 AN XY: 70404

Gnomad AFR exome AF: 0.000777

Gnomad AMR exome AF: 0.00891

Gnomad ASJ exome AF: 0.00155

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00341

Gnomad FIN exome AF: 0.00108

Gnomad NFE exome AF: 0.00281

Gnomad OTH exome AF: 0.00329

GnomAD4 exome AF: 0.00249 AC: 2940 AN: 1178748 Hom.: 52 Cov.: 30 AF XY: 0.00272 AC XY: 1597 AN XY: 586840

Gnomad4 AFR exome AF: 0.000579

Gnomad4 AMR exome AF: 0.0101

Gnomad4 ASJ exome AF: 0.00234

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00546

Gnomad4 FIN exome AF: 0.00205

Gnomad4 NFE exome AF: 0.00210

Gnomad4 OTH exome AF: 0.00304

GnomAD4 genome AF: 0.00380 AC: 555 AN: 146176 Hom.: 2 Cov.: 0 AF XY: 0.00410 AC XY: 292 AN XY: 71304

Gnomad4 AFR AF: 0.000873

Gnomad4 AMR AF: 0.0117

Gnomad4 ASJ AF: 0.00330

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00459

Gnomad4 FIN AF: 0.00109

Gnomad4 NFE AF: 0.00434

Gnomad4 OTH AF: 0.00847

Alfa AF: 0.00103 Hom.: 640

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs70988830; hg19: chr5-41033931;