rs502658

Variant names:

• chr1-200960877-T-C
• rs502658
• ENST00000435735.2:n.2361+444T>C

Variant summary

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

The NR_147176.1(MROH3P):​n.1837+444T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,150 control chromosomes in the GnomAD database, including 1,917 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 0.16 (1917 hom., cov: 32)
• Consequence: MROH3P NR_147176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 10 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH3P	NR_147176.1		n.1837+444T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH3P	ENST00000435735.2	TSL:6	n.2361+444T>C		intron	N/A
	ENSG00000293444	ENST00000635940.1	TSL:5	n.2109+444T>C		intron	N/A
	ENSG00000293444	ENST00000723937.1		n.961+444T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23704 AN: 152032 Hom.: 1914 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.156 AC: 23715 AN: 152150 Hom.: 1917 Cov.: 32 AF XY: 0.153 AC XY: 11358 AN XY: 74394

African (AFR) AF: 0.123 AC: 5108 AN: 41504

American (AMR) AF: 0.143 AC: 2181 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.118 AC: 611 AN: 5186

South Asian (SAS) AF: 0.145 AC: 700 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1570 AN: 10582

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12289 AN: 68000

Other (OTH) AF: 0.163 AC: 342 AN: 2102

Alfa AF: 0.174 Hom.: 7528

Bravo AF: 0.153

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.6
DANN	Benign	0.89
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs502658; hg19: chr1-200930005;