dbSNP rs7086888: MANCR:n.169-42910T>C (chr10-4634004-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.224

Publications

6 publications found

Variant links:

Genes affected

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

MANCR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MANCR	ENST00000700874.2 link	n.169-42910T>C	intron_variant	Intron 1 of 2
MANCR	ENST00000737867.1 link	n.122-42910T>C	intron_variant	Intron 1 of 3
MANCR	ENST00000737868.1 link	n.282+14736T>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17554

AN:

151876

Hom.:

1635

Cov.:

show subpopulations

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.:

AF XY:

0.114

AC XY:

8459

AN XY:

74302

show subpopulations

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:

AN:

3468

East Asian (EAS)

AF:

0.00834

AC:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0666

AC:

4526

AN:

67984

Other (OTH)

AF:

0.0977

AC:

206

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

730

1459

2189

2918

3648

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.0

(source)

DANN

Benign

0.70

PhyloP100

-0.22

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over