rs867852

Variant names:

• chr1-200948175-C-T
• rs867852
• ENST00000435735.2:n.1291C>T

Variant summary

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

The NR_147176.1(MROH3P):​n.596C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,104 control chromosomes in the GnomAD database, including 37,185 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 0.67 (36995 hom., cov: 27)
  • Exomes 𝑓: 0.83 (190 hom.)
• Consequence: MROH3P NR_147176.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 5 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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_147176.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH3P	NR_147176.1		n.596C>T		non_coding_transcript_exon	Exon 5 of 16

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH3P	ENST00000435735.2	TSL:6	n.1291C>T		non_coding_transcript_exon	Exon 12 of 22
	ENSG00000293444	ENST00000635940.1	TSL:5	n.868C>T		non_coding_transcript_exon	Exon 7 of 18

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101385 AN: 151424 Hom.: 36979 Cov.: 27

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.706

GnomAD4 exome AF: 0.826 AC: 464 AN: 562 Hom.: 190 Cov.: 0 AF XY: 0.831 AC XY: 299 AN XY: 360

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.821 AC: 353 AN: 430

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.856 AC: 101 AN: 118

Other (OTH) AF: 0.500 AC: 3 AN: 6

GnomAD4 genome AF: 0.669 AC: 101423 AN: 151542 Hom.: 36995 Cov.: 27 AF XY: 0.674 AC XY: 49914 AN XY: 74020

African (AFR) AF: 0.350 AC: 14440 AN: 41256

American (AMR) AF: 0.768 AC: 11687 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2521 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3852 AN: 5116

South Asian (SAS) AF: 0.771 AC: 3680 AN: 4770

European-Finnish (FIN) AF: 0.823 AC: 8643 AN: 10504

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54203 AN: 67910

Other (OTH) AF: 0.707 AC: 1479 AN: 2092

Alfa AF: 0.718 Hom.: 9220

Bravo AF: 0.652

Asia WGS AF: 0.733 AC: 2551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.5
DANN	Benign	0.79
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs867852; hg19: chr1-200917303;