rs11584383

Variant names:

• chr1-200966738-T-C
• rs11584383
• ENST00000435735.2:n.*202T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-200966738-T-C
• chr1-200966738-T-G

Variant summary

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

The ENST00000435735.2(MROH3P):​n.*202T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,268 control chromosomes in the GnomAD database, including 4,548 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 0.23 (4545 hom., cov: 33)
  • Exomes 𝑓: 0.37 (3 hom.)
• Consequence: MROH3P ENST00000435735.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772
• Publications: 70 publications found

Genes affected

MROH3P (HGNC:33122): (maestro heat like repeat family member 3, pseudogene)

ENSG00000293444 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435735.2. 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
	MROH3P	NR_147176.1		n.*70T>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH3P	ENST00000435735.2	TSL:6	n.*202T>C		downstream_gene	N/A
	ENSG00000293444	ENST00000635940.1	TSL:5	n.*70T>C		downstream_gene	N/A
	ENSG00000293444	ENST00000723937.1		n.*55T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35545 AN: 152112 Hom.: 4540 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.368 AC: 14 AN: 38 Hom.: 3 AF XY: 0.308 AC XY: 8 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.357 AC: 5 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.444 AC: 8 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.234 AC: 35559 AN: 152230 Hom.: 4545 Cov.: 33 AF XY: 0.228 AC XY: 16954 AN XY: 74426

African (AFR) AF: 0.193 AC: 8019 AN: 41544

American (AMR) AF: 0.167 AC: 2562 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3472

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5188

South Asian (SAS) AF: 0.131 AC: 633 AN: 4828

European-Finnish (FIN) AF: 0.236 AC: 2503 AN: 10588

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20044 AN: 67996

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.264 Hom.: 21272

Bravo AF: 0.228

Asia WGS AF: 0.0790 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs11584383; hg19: chr1-200935866;