5-41033829-C-CTATT

Position:

• chr5-41033829-C-CTATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000399564.5(MROH2B):​c.2241+8_2241+9insAATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,157,850 control chromosomes in the GnomAD database, including 41,970 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.23 (4389 hom., cov: 0)
  • Exomes 𝑓: 0.18 (41970 hom.)
  • Failed GnomAD Quality Control
• 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MROH2B	NM_173489.5	c.2241+8_2241+9insAATA		intron_variant		ENST00000399564.5	NP_775760.3
MROH2B	XM_011513952.2	c.2241+8_2241+9insAATA		intron_variant			XP_011512254.1
MROH2B	XM_011513953.2	c.2055+8_2055+9insAATA		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+9insAATA		intron_variant		1	NM_173489.5	ENSP00000382476	P1
MROH2B	ENST00000506092.6	c.906+8_906+9insAATA		intron_variant		2		ENSP00000441504
MROH2B	ENST00000503890.5	n.1203+8_1203+9insAATA		intron_variant, non_coding_transcript_variant		2
MROH2B	ENST00000515297.5	n.1629+8_1629+9insAATA		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 33869 AN: 145860 Hom.: 4390 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.232

GnomAD3 exomes AF: 0.222 AC: 29395 AN: 132376 Hom.: 5992 AF XY: 0.222 AC XY: 15656 AN XY: 70404

Gnomad AFR exome AF: 0.185

Gnomad AMR exome AF: 0.208

Gnomad ASJ exome AF: 0.302

Gnomad EAS exome AF: 0.139

Gnomad SAS exome AF: 0.207

Gnomad FIN exome AF: 0.227

Gnomad NFE exome AF: 0.241

Gnomad OTH exome AF: 0.237

GnomAD4 exome AF: 0.177 AC: 205099 AN: 1157850 Hom.: 41970 Cov.: 30 AF XY: 0.181 AC XY: 104356 AN XY: 576018

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.202

Gnomad4 ASJ exome AF: 0.274

Gnomad4 EAS exome AF: 0.120

Gnomad4 SAS exome AF: 0.198

Gnomad4 FIN exome AF: 0.225

Gnomad4 NFE exome AF: 0.172

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.232 AC: 33874 AN: 145972 Hom.: 4389 Cov.: 0 AF XY: 0.230 AC XY: 16374 AN XY: 71182

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.233

Alfa AF: 0.226 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;