1-200923009-T-C

Position:

• chr1-200923009-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435735.2(MROH3P):​n.569+248T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

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=-0.95).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MROH3P	ENST00000435735.2	n.569+248T>C		intron_variant, non_coding_transcript_variant
	ENST00000635940.1	n.71+248T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.554

Alfa AF: 0.613 Hom.: 66685

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs296547; hg19: chr1-200892137;