NM_001163629.2:c.1596+7496A>C

Variant names:

• chr1-171005770-A-C
• rs3853181
• NM_001163629.2:c.1596+7496A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001163629.2(MROH9):​c.1596+7496A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,020 control chromosomes in the GnomAD database, including 8,904 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 0.29 (8904 hom., cov: 32)
• Consequence: MROH9 NM_001163629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 publications found

Genes affected

MROH9 (HGNC:26287): (maestro heat like repeat family member 9)

ENSG00000231424 (HGNC:40240):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001163629.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH9	NM_001163629.2	MANE Select	c.1596+7496A>C		intron	N/A	NP_001157101.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH9	ENST00000367759.9	TSL:5 MANE Select	c.1596+7496A>C		intron	N/A	ENSP00000356733.4
	MROH9	ENST00000426136.1	TSL:5	c.414+7496A>C		intron	N/A	ENSP00000403697.1
	ENSG00000231424	ENST00000653116.1		n.543-141084T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43876 AN: 151902 Hom.: 8872 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.289 AC: 43963 AN: 152020 Hom.: 8904 Cov.: 32 AF XY: 0.283 AC XY: 21006 AN XY: 74324

African (AFR) AF: 0.580 AC: 24023 AN: 41394

American (AMR) AF: 0.215 AC: 3278 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3472

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5164

South Asian (SAS) AF: 0.155 AC: 747 AN: 4826

European-Finnish (FIN) AF: 0.133 AC: 1410 AN: 10586

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12991 AN: 67994

Other (OTH) AF: 0.278 AC: 586 AN: 2106

Alfa AF: 0.222 Hom.: 6633

Bravo AF: 0.306

Asia WGS AF: 0.114 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.4
DANN	Benign	0.92
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3853181; hg19: chr1-170974911;