1-200923009-T-C

Variant names:

• chr1-200923009-T-C
• rs296547
• ENST00000435735.2:n.569+248T>C

Variant summary

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

The ENST00000435735.2(MROH3P):​n.569+248T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,048 control chromosomes in the GnomAD database, including 22,740 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 0.53 (22740 hom., cov: 32)
• Consequence: MROH3P ENST00000435735.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 44 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MROH3P	ENST00000435735.2	n.569+248T>C		intron_variant	Intron 6 of 21	6
ENSG00000293444	ENST00000635940.1	n.71+248T>C		intron_variant	Intron 1 of 17	5
ENSG00000293444	ENST00000806392.1	n.849+1148T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80452 AN: 151930 Hom.: 22727 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.529 AC: 80484 AN: 152048 Hom.: 22740 Cov.: 32 AF XY: 0.527 AC XY: 39196 AN XY: 74312

African (AFR) AF: 0.319 AC: 13236 AN: 41502

American (AMR) AF: 0.620 AC: 9465 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2135 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1896 AN: 5156

South Asian (SAS) AF: 0.464 AC: 2233 AN: 4812

European-Finnish (FIN) AF: 0.628 AC: 6624 AN: 10554

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43036 AN: 67970

Other (OTH) AF: 0.554 AC: 1170 AN: 2112

Alfa AF: 0.599 Hom.: 129646

Bravo AF: 0.521

Asia WGS AF: 0.394 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.34
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs296547; hg19: chr1-200892137;