rs7086888

Variant names:

• chr10-4634004-A-G
• rs7086888
• ENST00000700874.2:n.169-42910T>C

Variant summary

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

The ENST00000700874.2(MANCR):​n.169-42910T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,994 control chromosomes in the GnomAD database, including 1,642 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 0.12 (1642 hom., cov: 32)
• Consequence: MANCR ENST00000700874.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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.169-42910T>C		intron	N/A
	MANCR	ENST00000737867.1		n.122-42910T>C		intron	N/A
	MANCR	ENST00000737868.1		n.282+14736T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17554 AN: 151876 Hom.: 1635 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.00832

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0450

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.116 AC: 17601 AN: 151994 Hom.: 1642 Cov.: 32 AF XY: 0.114 AC XY: 8459 AN XY: 74302

African (AFR) AF: 0.259 AC: 10712 AN: 41406

American (AMR) AF: 0.0626 AC: 956 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3468

East Asian (EAS) AF: 0.00834 AC: 43 AN: 5154

South Asian (SAS) AF: 0.116 AC: 557 AN: 4820

European-Finnish (FIN) AF: 0.0450 AC: 476 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0666 AC: 4526 AN: 67984

Other (OTH) AF: 0.0977 AC: 206 AN: 2108

Alfa AF: 0.0919 Hom.: 1950

Bravo AF: 0.122

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs7086888; hg19: chr10-4676196;