dbSNP rs6890173: LOC102724458:n.192-4133T>G (chr5-163716979-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_427816.3(LOC102724458):n.192-4133T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,234 control chromosomes in the GnomAD database, including 1,843 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 0.15 ( 1843 hom., cov: 32)

Consequence

LOC102724458
XR_427816.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.124

Publications

1 publications found

Variant links:

Genes affected

LOC102724458 (HGNC:):

LOC102724458 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC102724458	XR_427816.3 link	n.192-4133T>G	intron_variant	Intron 2 of 4
LOC102724458	XR_941163.2 link	n.259+3330T>G	intron_variant	Intron 3 of 5
LOC102724458	XR_941164.2 link	n.746+3330T>G	intron_variant	Intron 3 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23141

AN:

152116

Hom.:

1839

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.00385

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.164

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

GnomAD4 genome

AF:

0.152

AC:

23160

AN:

152234

Hom.:

1843

Cov.:

AF XY:

0.149

AC XY:

11120

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.162

AC:

6745

AN:

41538

American (AMR)

AF:

0.115

AC:

1762

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

478

AN:

3472

East Asian (EAS)

AF:

0.00386

AC:

AN:

5186

South Asian (SAS)

AF:

0.121

AC:

583

AN:

4822

European-Finnish (FIN)

AF:

0.145

AC:

1537

AN:

10604

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11447

AN:

67998

Other (OTH)

AF:

0.164

AC:

346

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1017

2034

3050

4067

5084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.154

Hom.:

256

Bravo

AF:

0.146

Asia WGS

AF:

0.0620

AC:

216

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.7

(source)

DANN

Benign

0.60

PhyloP100

0.12

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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