Genetic Variant MANCR:n.169-22279T>C (chr10-4613373-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.169-22279T>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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28

Publications

16 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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.169-22279T>C	intron_variant	Intron 1 of 2
MANCR	ENST00000737867.1 link	n.122-22279T>C	intron_variant	Intron 1 of 3
MANCR	ENST00000737868.1 link	n.283-22279T>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.759

AC:

115269

AN:

151918

Hom.:

44054

Cov.:

show subpopulations

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.:

AF XY:

0.766

AC XY:

56956

AN XY:

74308

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1400

2800

4199

5599

6999

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

862

1724

2586

3448

4310

<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:

0.771

Hom.:

162299

Bravo

AF:

0.756

Asia WGS

AF:

0.893

AC:

3097

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

(source)

DANN

Benign

0.39

PhyloP100

-2.3

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