Genetic Variant LOC102724542:n.497+43680T>C (chr2-81592427-T-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_187691.1(LOC102724542):n.497+43680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,040 control chromosomes in the GnomAD database, including 5,111 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 0.24 ( 5111 hom., cov: 32)

Consequence

LOC102724542
NR_187691.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.143

Publications

2 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC102724542	NR_187691.1 link	n.497+43680T>C	intron_variant	Intron 2 of 3
LOC102724542	NR_187692.1 link	n.575+12818T>C	intron_variant	Intron 3 of 4
LOC102724542	NR_187693.1 link	n.497+43680T>C	intron_variant	Intron 2 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37169

AN:

151922

Hom.:

5104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.478

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.323

Gnomad OTH

AF:

0.230

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

GnomAD4 genome

AF:

0.245

AC:

37194

AN:

152040

Hom.:

5111

Cov.:

AF XY:

0.240

AC XY:

17825

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.132

AC:

5491

AN:

41538

American (AMR)

AF:

0.207

AC:

3152

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

970

AN:

3464

East Asian (EAS)

AF:

0.168

AC:

868

AN:

5172

South Asian (SAS)

AF:

0.121

AC:

585

AN:

4816

European-Finnish (FIN)

AF:

0.305

AC:

3215

AN:

10552

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.323

AC:

21923

AN:

67928

Other (OTH)

AF:

0.229

AC:

485

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1378

2756

4134

5512

6890

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<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:

0.293

Hom.:

9503

Bravo

AF:

0.235

Asia WGS

AF:

0.150

AC:

520

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.3

(source)

DANN

Benign

0.50

PhyloP100

-0.14

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