5-41033829-C-CTATCTATCTATCTATT

Variant names:

• chr5-41033829-C-CTATCTATCTATCTATT
• rs70988830
• NM_173489.5:c.2241+8_2241+9insAATAGATAGATAGATA

Variant summary

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

The NM_173489.5(MROH2B):​c.2241+8_2241+9insAATAGATAGATAGATA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0035 (10 hom., cov: 0)
  • Exomes 𝑓: 0.0021 (289 hom.)
  • Failed GnomAD Quality Control
• Consequence: MROH2B NM_173489.5 splice_region, 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 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MROH2B	NM_173489.5	c.2241+8_2241+9insAATAGATAGATAGATA		splice_region_variant, intron_variant	Intron 22 of 41	ENST00000399564.5	NP_775760.3
MROH2B	XM_011513952.2	c.2241+8_2241+9insAATAGATAGATAGATA		splice_region_variant, intron_variant	Intron 22 of 42		XP_011512254.1
MROH2B	XM_011513953.2	c.2055+8_2055+9insAATAGATAGATAGATA		splice_region_variant, intron_variant	Intron 21 of 40		XP_011512255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MROH2B	ENST00000399564.5	c.2241+8_2241+9insAATAGATAGATAGATA		splice_region_variant, intron_variant	Intron 22 of 41	1	NM_173489.5	ENSP00000382476.4
MROH2B	ENST00000506092.6	c.906+8_906+9insAATAGATAGATAGATA		splice_region_variant, intron_variant	Intron 12 of 31	2		ENSP00000441504.1
MROH2B	ENST00000503890.5	n.1203+8_1203+9insAATAGATAGATAGATA		splice_region_variant, intron_variant	Intron 10 of 30	2
MROH2B	ENST00000515297.5	n.1629+8_1629+9insAATAGATAGATAGATA		splice_region_variant, intron_variant	Intron 16 of 35	5

Frequencies

GnomAD3 genomes AF: 0.00349 AC: 510 AN: 146060 Hom.: 10 Cov.: 0

Gnomad AFR AF: 0.00193

Gnomad AMI AF: 0.00228

Gnomad AMR AF: 0.00505

Gnomad ASJ AF: 0.00270

Gnomad EAS AF: 0.00119

Gnomad SAS AF: 0.00437

Gnomad FIN AF: 0.00526

Gnomad MID AF: 0.00329

Gnomad NFE AF: 0.00398

Gnomad OTH AF: 0.00302

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00212 AC: 2497 AN: 1178764 Hom.: 289 Cov.: 30 AF XY: 0.00223 AC XY: 1307 AN XY: 586852

Gnomad4 AFR exome AF: 0.00152

Gnomad4 AMR exome AF: 0.00320

Gnomad4 ASJ exome AF: 0.00387

Gnomad4 EAS exome AF: 0.00167

Gnomad4 SAS exome AF: 0.00206

Gnomad4 FIN exome AF: 0.00439

Gnomad4 NFE exome AF: 0.00194

Gnomad4 OTH exome AF: 0.00246

GnomAD4 genome AF: 0.00350 AC: 511 AN: 146174 Hom.: 10 Cov.: 0 AF XY: 0.00356 AC XY: 254 AN XY: 71302

Gnomad4 AFR AF: 0.00195

Gnomad4 AMR AF: 0.00504

Gnomad4 ASJ AF: 0.00270

Gnomad4 EAS AF: 0.00119

Gnomad4 SAS AF: 0.00437

Gnomad4 FIN AF: 0.00526

Gnomad4 NFE AF: 0.00398

Gnomad4 OTH AF: 0.00299

Alfa AF: 0.00207 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;