1-200920705-T-C

Variant names:

• chr1-200920705-T-C
• rs296543
• ENST00000435735.2:n.153+186T>C

Variant summary

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

The ENST00000435735.2(MROH3P):​n.153+186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,102 control chromosomes in the GnomAD database, including 43,167 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 0.75 (43167 hom., cov: 31)
• Consequence: MROH3P ENST00000435735.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH3P	ENST00000435735.2	TSL:6	n.153+186T>C		intron	N/A
	ENSG00000293444	ENST00000806392.1		n.516+186T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114270 AN: 151984 Hom.: 43128 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.752 AC: 114358 AN: 152102 Hom.: 43167 Cov.: 31 AF XY: 0.756 AC XY: 56246 AN XY: 74360

African (AFR) AF: 0.790 AC: 32787 AN: 41508

American (AMR) AF: 0.802 AC: 12273 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2643 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4093 AN: 5146

South Asian (SAS) AF: 0.819 AC: 3934 AN: 4804

European-Finnish (FIN) AF: 0.761 AC: 8062 AN: 10590

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48247 AN: 67974

Other (OTH) AF: 0.750 AC: 1582 AN: 2108

Alfa AF: 0.724 Hom.: 139128

Bravo AF: 0.754

Asia WGS AF: 0.778 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.50
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs296543; hg19: chr1-200889833;