Genetic Variant LOC105369165:n.49-128967G>A (chr2-53038991-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_187747.1(LOC105369165):n.49-128967G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 151,706 control chromosomes in the GnomAD database, including 37,895 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 0.69 ( 37895 hom., cov: 31)

Consequence

LOC105369165
NR_187747.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.465

Publications

9 publications found

Variant links:

Genes affected

LOC105369165 (HGNC:):

LOC105369165 links:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105369165	NR_187747.1 link	n.49-128967G>A	intron_variant	Intron 1 of 4
LOC105369165	NR_187748.1 link	n.49-128967G>A	intron_variant	Intron 1 of 6
LOC105369165	NR_187750.1 link	n.49-128967G>A	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.692

AC:

104893

AN:

151588

Hom.:

37836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.912

Gnomad AMI

AF:

0.452

Gnomad AMR

AF:

0.585

Gnomad ASJ

AF:

0.572

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.788

Gnomad FIN

AF:

0.675

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.640

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

GnomAD4 genome

AF:

0.692

AC:

105011

AN:

151706

Hom.:

37895

Cov.:

AF XY:

0.692

AC XY:

51292

AN XY:

74112

show subpopulations

African (AFR)

AF:

0.912

AC:

37848

AN:

41486

American (AMR)

AF:

0.584

AC:

8895

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.572

AC:

1979

AN:

3462

East Asian (EAS)

AF:

0.553

AC:

2847

AN:

5152

South Asian (SAS)

AF:

0.788

AC:

3797

AN:

4818

European-Finnish (FIN)

AF:

0.675

AC:

7101

AN:

10514

Middle Eastern (MID)

AF:

0.578

AC:

170

AN:

294

European-Non Finnish (NFE)

AF:

0.599

AC:

40603

AN:

67736

Other (OTH)

AF:

0.645

AC:

1359

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1502

3004

4505

6007

7509

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

810

1620

2430

3240

4050

<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:

0.618

Hom.:

100744

Bravo

AF:

0.687

Asia WGS

AF:

0.702

AC:

2432

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.28

(source)

DANN

Benign

0.58

PhyloP100

-0.47

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