Genetic Variant LOC105369165:n.49-100158C>G (chr2-53010182-G-C) – 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.49-100158C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,974 control chromosomes in the GnomAD database, including 37,125 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 ( 37125 hom., cov: 32)

Consequence

LOC105369165
NR_187747.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.421

Publications

7 publications found

Variant links:

Genes affected

LOC105369165 (HGNC:):

LOC105369165 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105369165	NR_187747.1 link	n.49-100158C>G	intron_variant	Intron 1 of 4
LOC105369165	NR_187748.1 link	n.49-100158C>G	intron_variant	Intron 1 of 6
LOC105369165	NR_187750.1 link	n.49-100158C>G	intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.689

AC:

104674

AN:

151856

Hom.:

37071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.861

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.578

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.790

Gnomad FIN

AF:

0.668

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.618

Gnomad OTH

AF:

0.644

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

GnomAD4 genome

AF:

0.690

AC:

104791

AN:

151974

Hom.:

37125

Cov.:

AF XY:

0.689

AC XY:

51165

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.861

AC:

35732

AN:

41504

American (AMR)

AF:

0.634

AC:

9661

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.578

AC:

2002

AN:

3466

East Asian (EAS)

AF:

0.510

AC:

2625

AN:

5152

South Asian (SAS)

AF:

0.790

AC:

3810

AN:

4820

European-Finnish (FIN)

AF:

0.668

AC:

7043

AN:

10540

Middle Eastern (MID)

AF:

0.554

AC:

163

AN:

294

European-Non Finnish (NFE)

AF:

0.618

AC:

41968

AN:

67938

Other (OTH)

AF:

0.648

AC:

1366

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1593

3186

4780

6373

7966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

820

1640

2460

3280

4100

<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:

0.623

Hom.:

16569

Bravo

AF:

0.687

Asia WGS

AF:

0.697

AC:

2423

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.7

(source)

DANN

Benign

0.73

PhyloP100

-0.42

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