rs7086888

Variant names:

• chr10-4634004-A-G
• rs7086888
• ENST00000700874.1:n.169-42910T>C

Variant summary

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

The ENST00000700874.1(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 ENST00000700874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MANCR	ENST00000700874.1	n.169-42910T>C		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.00834

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0450

Gnomad4 NFE AF: 0.0666

Gnomad4 OTH AF: 0.0977

Alfa AF: 0.0745 Hom.: 711

Bravo AF: 0.122

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7086888; hg19: chr10-4676196;