Genetic Variant NR_187747.1:n.49-126391A>G (chr2-53036415-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_187747.1(LOC105369165):n.49-126391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,094 control chromosomes in the GnomAD database, including 1,708 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 0.14 ( 1708 hom., cov: 32)

Consequence

LOC105369165
NR_187747.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145

Publications

3 publications found

Variant links:

Genes affected

LOC105369165 (HGNC:):

LOC105369165 links:

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new If you want to explore the variant's impact on the transcript NR_187747.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187747.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LOC105369165	NR_187747.1	n.49-126391A>G	intron	N/A
LOC105369165	NR_187748.1	n.49-126391A>G	intron	N/A
LOC105369165	NR_187750.1	n.49-126391A>G	intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21306

AN:

151976

Hom.:

1707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0784

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.0137

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.140

AC:

21311

AN:

152094

Hom.:

1708

Cov.:

AF XY:

0.142

AC XY:

10543

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.0783

AC:

3252

AN:

41516

American (AMR)

AF:

0.101

AC:

1549

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

608

AN:

3468

East Asian (EAS)

AF:

0.0133

AC:

AN:

5180

South Asian (SAS)

AF:

0.134

AC:

643

AN:

4814

European-Finnish (FIN)

AF:

0.233

AC:

2458

AN:

10560

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.179

AC:

12199

AN:

67966

Other (OTH)

AF:

0.124

AC:

261

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

941

1881

2822

3762

4703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.163

Hom.:

3522

Bravo

AF:

0.126

Asia WGS

AF:

0.0730

AC:

255

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.4

(source)

DANN

Benign

0.63

PhyloP100

-0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over