chr5-41033829-C-CTTATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_173489.5(MROH2B):​c.2241+8_2241+9insAATAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,178,452 control chromosomes in the GnomAD database, including 511 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.018 ( 47 hom., cov: 0)
Exomes 𝑓: 0.013 ( 511 hom. )
Failed GnomAD Quality Control

Consequence

MROH2B
NM_173489.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.238
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0131 (15463/1178452) while in subpopulation AMR AF= 0.0369 (1209/32764). AF 95% confidence interval is 0.0352. There are 511 homozygotes in gnomad4_exome. There are 8060 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 511 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MROH2BNM_173489.5 linkc.2241+8_2241+9insAATAA splice_region_variant, intron_variant Intron 22 of 41 ENST00000399564.5 NP_775760.3
MROH2BXM_011513952.2 linkc.2241+8_2241+9insAATAA splice_region_variant, intron_variant Intron 22 of 42 XP_011512254.1
MROH2BXM_011513953.2 linkc.2055+8_2055+9insAATAA 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
MROH2BENST00000399564.5 linkc.2241+8_2241+9insAATAA splice_region_variant, intron_variant Intron 22 of 41 1 NM_173489.5 ENSP00000382476.4 Q7Z745-1
MROH2BENST00000506092.6 linkc.906+8_906+9insAATAA splice_region_variant, intron_variant Intron 12 of 31 2 ENSP00000441504.1 F5GZ06
MROH2BENST00000503890.5 linkn.1203+8_1203+9insAATAA splice_region_variant, intron_variant Intron 10 of 30 2
MROH2BENST00000515297.5 linkn.1629+8_1629+9insAATAA splice_region_variant, intron_variant Intron 16 of 35 5

Frequencies

GnomAD3 genomes
AF:
0.0184
AC:
2690
AN:
146052
Hom.:
47
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00489
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0310
Gnomad ASJ
AF:
0.00659
Gnomad EAS
AF:
0.000198
Gnomad SAS
AF:
0.0181
Gnomad FIN
AF:
0.0209
Gnomad MID
AF:
0.00987
Gnomad NFE
AF:
0.0255
Gnomad OTH
AF:
0.0161
GnomAD3 exomes
AF:
0.0189
AC:
2497
AN:
132376
Hom.:
88
AF XY:
0.0187
AC XY:
1314
AN XY:
70404
show subpopulations
Gnomad AFR exome
AF:
0.00404
Gnomad AMR exome
AF:
0.0358
Gnomad ASJ exome
AF:
0.00310
Gnomad EAS exome
AF:
0.0000987
Gnomad SAS exome
AF:
0.0160
Gnomad FIN exome
AF:
0.0183
Gnomad NFE exome
AF:
0.0210
Gnomad OTH exome
AF:
0.0197
GnomAD4 exome
AF:
0.0131
AC:
15463
AN:
1178452
Hom.:
511
Cov.:
30
AF XY:
0.0137
AC XY:
8060
AN XY:
586674
show subpopulations
Gnomad4 AFR exome
AF:
0.00279
Gnomad4 AMR exome
AF:
0.0369
Gnomad4 ASJ exome
AF:
0.00351
Gnomad4 EAS exome
AF:
0.0000287
Gnomad4 SAS exome
AF:
0.0188
Gnomad4 FIN exome
AF:
0.0204
Gnomad4 NFE exome
AF:
0.0125
Gnomad4 OTH exome
AF:
0.0136
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0184
AC:
2690
AN:
146166
Hom.:
47
Cov.:
0
AF XY:
0.0179
AC XY:
1276
AN XY:
71298
show subpopulations
Gnomad4 AFR
AF:
0.00488
Gnomad4 AMR
AF:
0.0311
Gnomad4 ASJ
AF:
0.00659
Gnomad4 EAS
AF:
0.000198
Gnomad4 SAS
AF:
0.0179
Gnomad4 FIN
AF:
0.0209
Gnomad4 NFE
AF:
0.0255
Gnomad4 OTH
AF:
0.0154
Alfa
AF:
0.0120
Hom.:
640

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs70988830; hg19: chr5-41033931; API