ENST00000700874.1:n.169-22279T>C

Variant names:

• chr10-4613373-A-G
• rs10458787
• ENST00000700874.2:n.169-22279T>C

Variant summary

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

The ENST00000700874.2(MANCR):​n.169-22279T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,036 control chromosomes in the GnomAD database, including 44,081 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 0.76 (44081 hom., cov: 31)
• Consequence: MANCR ENST00000700874.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 16 publications found

Genes affected

MANCR (HGNC:44678): (mitotically associated long non coding RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000700874.2. 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
	MANCR	ENST00000700874.2		n.169-22279T>C		intron	N/A
	MANCR	ENST00000737867.1		n.122-22279T>C		intron	N/A
	MANCR	ENST00000737868.1		n.283-22279T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115269 AN: 151918 Hom.: 44054 Cov.: 31

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.759 AC: 115349 AN: 152036 Hom.: 44081 Cov.: 31 AF XY: 0.766 AC XY: 56956 AN XY: 74308

African (AFR) AF: 0.686 AC: 28419 AN: 41432

American (AMR) AF: 0.783 AC: 11967 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3000 AN: 3466

East Asian (EAS) AF: 0.995 AC: 5152 AN: 5176

South Asian (SAS) AF: 0.878 AC: 4232 AN: 4820

European-Finnish (FIN) AF: 0.787 AC: 8315 AN: 10564

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51657 AN: 67984

Other (OTH) AF: 0.778 AC: 1641 AN: 2110

Alfa AF: 0.771 Hom.: 162299

Bravo AF: 0.756

Asia WGS AF: 0.893 AC: 3097 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10458787; hg19: chr10-4655565;