dbSNP rs2165953: MANCR:n.129+3699C>T (chr10-4674350-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430998.8(MANCR):n.129+3699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,094 control chromosomes in the GnomAD database, including 38,577 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 0.70 ( 38577 hom., cov: 33)

Consequence

MANCR
ENST00000430998.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.324

Variant links:

Genes affected

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

MANCR links:

LINC00705 (HGNC:27874): (long intergenic non-protein coding RNA 705)

LINC00705 links:

LOC105376373 (HGNC:):

LOC105376373 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MANCR	NR_024475.1 link	n.22+3699C>T	intron_variant	Intron 1 of 3
LOC105376373	XR_001747338.2 link	n.130-2315G>A	intron_variant	Intron 1 of 3
LOC105376373	XR_007062036.1 link	n.130-2315G>A	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MANCR	ENST00000430998.8 link	n.129+3699C>T	intron_variant	Intron 1 of 3	1
MANCR	ENST00000449712.2 link	n.84+3699C>T	intron_variant	Intron 1 of 4	3
LINC00705	ENST00000653457.1 link	n.578-2315G>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

106245

AN:

151974

Hom.:

38574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.756

Gnomad AMR

AF:

0.790

Gnomad ASJ

AF:

0.728

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.792

Gnomad FIN

AF:

0.796

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.773

Gnomad OTH

AF:

0.700

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

GnomAD4 genome

AF:

0.699

AC:

106278

AN:

152094

Hom.:

38577

Cov.:

AF XY:

0.704

AC XY:

52385

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.482

AC:

19960

AN:

41440

American (AMR)

AF:

0.790

AC:

12078

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.728

AC:

2526

AN:

3472

East Asian (EAS)

AF:

0.876

AC:

4536

AN:

5180

South Asian (SAS)

AF:

0.793

AC:

3827

AN:

4828

European-Finnish (FIN)

AF:

0.796

AC:

8438

AN:

10594

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.773

AC:

52550

AN:

67982

Other (OTH)

AF:

0.696

AC:

1468

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1523

3046

4569

6092

7615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.745

Hom.:

157648

Bravo

AF:

0.688

Asia WGS

AF:

0.822

AC:

2854

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.16

(source)

DANN

Benign

0.74

PhyloP100

-0.32

Splicing

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

Publications

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rs2165953

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over