rs1500474

chr2-233800894-C-T

Variant summary

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

The NM_001394639.1(MROH2A):c.1560+579C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,900 control chromosomes in the GnomAD database, including 10,694 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 0.34 (10694 hom., cov: 31)
• Consequence: MROH2A NM_001394639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

MROH2A (HGNC:27936): (maestro heat like repeat family member 2A) This gene encodes a HEAT-domain-containing protein. The function of the encoded protein has not been characterized. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH2A	NM_001394639.1	c.1560+579C>T		intron_variant		ENST00000389758.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH2A	ENST00000389758.4	c.1560+579C>T		intron_variant		5	NM_001394639.1	A2
MROH2A	ENST00000610772.4	c.1569+579C>T		intron_variant		5		P4
MROH2A	ENST00000477506.2	n.334+579C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51312 AN: 151782 Hom.: 10671 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.338 AC: 51386 AN: 151900 Hom.: 10694 Cov.: 31 AF XY: 0.336 AC XY: 24924 AN XY: 74272

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.325

Alfa AF: 0.243 Hom.: 6587

Bravo AF: 0.366

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.9
Dann	Benign	0.63

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: rs1500474; hg19: chr2-234709540;