Genetic Variant LOC105373523:n.542-4902A>G (chr2-104120188-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 XR_923127.1(LOC105373523):n.542-4902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 152,240 control chromosomes in the GnomAD database, including 1,021 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 0.089 ( 1021 hom., cov: 32)

Consequence

LOC105373523
XR_923127.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

0 publications found

Variant links:

Genes affected

LOC105373523 (HGNC:):

LOC105373523 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373523	XR_923127.1 link	n.542-4902A>G		intron_variant	Intron 5 of 6
LOC105373523	XR_923128.1 link	n.538-4902A>G		intron_variant	Intron 5 of 6

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0886

AC:

13473

AN:

152122

Hom.:

1017

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0211

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0432

Gnomad EAS

AF:

0.411

Gnomad SAS

AF:

0.0706

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0950

Gnomad OTH

AF:

0.0841

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

GnomAD4 genome

AF:

0.0886

AC:

13482

AN:

152240

Hom.:

1021

Cov.:

AF XY:

0.0924

AC XY:

6875

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0210

AC:

873

AN:

41568

American (AMR)

AF:

0.126

AC:

1926

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0432

AC:

150

AN:

3472

East Asian (EAS)

AF:

0.411

AC:

2127

AN:

5180

South Asian (SAS)

AF:

0.0709

AC:

342

AN:

4824

European-Finnish (FIN)

AF:

0.125

AC:

1329

AN:

10602

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0951

AC:

6464

AN:

67992

Other (OTH)

AF:

0.0828

AC:

175

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

608

1216

1825

2433

3041

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.0932

Hom.:

287

Bravo

AF:

0.0892

Asia WGS

AF:

0.210

AC:

727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.60

(source)

DANN

Benign

0.74

PhyloP100

-1.1

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