rs502658

Positions:

• chr1-200960877-T-C

Variant summary

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

The NR_147176.1(MROH3P):​n.1837+444T>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 0.156 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH3P	NR_147176.1	n.1837+444T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH3P	ENST00000435735.2	n.2361+444T>C		intron_variant, non_coding_transcript_variant
	ENST00000635940.1	n.2109+444T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.163

Alfa AF: 0.178 Hom.: 3338

Bravo AF: 0.153

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs502658; hg19: chr1-200930005;