rs4915464

Variant names:

• chr1-200923922-G-C
• rs4915464
• ENST00000435735.2:n.569+1161G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-200923922-G-C
• chr1-200923922-G-T

Variant summary

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

The ENST00000806392.1(ENSG00000293444):​n.849+2061G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,022 control chromosomes in the GnomAD database, including 6,369 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 0.26 (6369 hom., cov: 32)
• Consequence: ENSG00000293444 ENST00000806392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806392.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH3P	ENST00000435735.2	TSL:6	n.569+1161G>C		intron	N/A
	ENSG00000293444	ENST00000635940.1	TSL:5	n.71+1161G>C		intron	N/A
	ENSG00000293444	ENST00000806392.1		n.849+2061G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40237 AN: 151904 Hom.: 6354 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.265 AC: 40251 AN: 152022 Hom.: 6369 Cov.: 32 AF XY: 0.267 AC XY: 19805 AN XY: 74276

African (AFR) AF: 0.0937 AC: 3889 AN: 41498

American (AMR) AF: 0.398 AC: 6075 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3468

East Asian (EAS) AF: 0.156 AC: 805 AN: 5170

South Asian (SAS) AF: 0.277 AC: 1332 AN: 4808

European-Finnish (FIN) AF: 0.317 AC: 3340 AN: 10536

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22551 AN: 67966

Other (OTH) AF: 0.303 AC: 640 AN: 2112

Alfa AF: 0.186 Hom.: 408

Bravo AF: 0.264

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.52
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4915464; hg19: chr1-200893050;