rs867852

chr1-200948175-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH3P	NR_147176.1	n.596C>T		non_coding_transcript_exon_variant	5/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH3P	ENST00000435735.2	n.1291C>T		non_coding_transcript_exon_variant	12/22
	ENST00000635940.1	n.868C>T		non_coding_transcript_exon_variant	7/18	5

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.821

Gnomad4 NFE exome AF: 0.856

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.707

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	8.5
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867852; hg19: chr1-200917303;