rs7086888

Positions:

• chr10-4634004-A-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MANCR	ENST00000700874.1	n.169-42910T>C		intron_variant, non_coding_transcript_variant

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;