dbSNP rs12615721: LOC102724542:n.497+80655G>A (chr2-81629402-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 NR_187691.1(LOC102724542):n.497+80655G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,052 control chromosomes in the GnomAD database, including 1,878 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 0.13 ( 1878 hom., cov: 32)

Consequence

LOC102724542
NR_187691.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62

Publications

6 publications found

Variant links:

Genes affected

LOC102724542 (HGNC:):

LOC102724542 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC102724542	NR_187691.1 link	n.497+80655G>A	intron_variant	Intron 2 of 3
LOC102724542	NR_187692.1 link	n.575+49793G>A	intron_variant	Intron 3 of 4
LOC102724542	NR_187693.1 link	n.497+80655G>A	intron_variant	Intron 2 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20313

AN:

151934

Hom.:

1863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.0742

Gnomad FIN

AF:

0.0436

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.0782

Gnomad OTH

AF:

0.135

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

GnomAD4 genome

AF:

0.134

AC:

20370

AN:

152052

Hom.:

1878

Cov.:

AF XY:

0.131

AC XY:

9762

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.258

AC:

10679

AN:

41452

American (AMR)

AF:

0.105

AC:

1599

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

567

AN:

3466

East Asian (EAS)

AF:

0.176

AC:

910

AN:

5172

South Asian (SAS)

AF:

0.0751

AC:

361

AN:

4810

European-Finnish (FIN)

AF:

0.0436

AC:

461

AN:

10580

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0782

AC:

5315

AN:

67988

Other (OTH)

AF:

0.136

AC:

286

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

843

1686

2529

3372

4215

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.0989

Hom.:

2991

Bravo

AF:

0.143

Asia WGS

AF:

0.133

AC:

460

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.045

(source)

DANN

Benign

0.43

PhyloP100

-1.6

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