20-37144941-C-T

Variant summary

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

The NM_152503.8(MROH8):c.1211-1100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,140 control chromosomes in the GnomAD database, including 12,032 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 0.39 (12032 hom., cov: 33)
• Consequence: MROH8 NM_152503.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

MROH8 (HGNC:16125): (maestro heat like repeat family member 8) The protein encoded by this gene belongs to the maestro heat-like repeat family. The exact function of this gene is not known, however, in a genome-wide association study using hippocampal atrophy as a quantitative trait, this gene has been associated with Alzheimer's disease (PMID:19668339). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH8	NM_152503.8	c.1211-1100G>A		intron_variant		ENST00000710289.2
MROH8	NM_213631.3	c.1211-1100G>A		intron_variant
MROH8	NM_213632.3	c.1106-1100G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH8	ENST00000343811.10	c.1211-1100G>A		intron_variant		1		P2
MROH8	ENST00000400440.7	c.1211-1100G>A		intron_variant		1		A2
MROH8	ENST00000421643.2	c.1106-1100G>A		intron_variant		2		A2
MROH8	ENST00000422138.2	c.1106-1100G>A		intron_variant		3		A2

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59544 AN: 152022 Hom.: 12028 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.392 AC: 59577 AN: 152140 Hom.: 12032 Cov.: 33 AF XY: 0.392 AC XY: 29165 AN XY: 74362

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.415

Alfa AF: 0.422 Hom.: 6562

Bravo AF: 0.397

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.068
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1780682; hg19: chr20-35773344;