Genetic Variant LOC124903820:n.996+674A>G (chr1-1159358-A-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_007065350.1(LOC124903820):n.996+674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,008 control chromosomes in the GnomAD database, including 28,796 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 0.61 ( 28796 hom., cov: 33)

Consequence

LOC124903820
XR_007065350.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.960

Publications

7 publications found

Variant links:

COSMIC-nc: COSV52468699

Genes affected

LOC124903820 (HGNC:):

LOC124903820 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=-0.97).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903820	XR_007065350.1 link	n.996+674A>G		intron_variant	Intron 1 of 1
LOC124903820	XR_007065351.1 link	n.278+674A>G		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.610

AC:

92583

AN:

151890

Hom.:

28762

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.724

Gnomad AMR

AF:

0.731

Gnomad ASJ

AF:

0.698

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.672

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.635

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

GnomAD4 genome

AF:

0.610

AC:

92662

AN:

152008

Hom.:

28796

Cov.:

AF XY:

0.610

AC XY:

45319

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.517

AC:

21445

AN:

41470

American (AMR)

AF:

0.731

AC:

11183

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.698

AC:

2419

AN:

3468

East Asian (EAS)

AF:

0.537

AC:

2764

AN:

5148

South Asian (SAS)

AF:

0.672

AC:

3248

AN:

4832

European-Finnish (FIN)

AF:

0.576

AC:

6080

AN:

10548

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.638

AC:

43334

AN:

67934

Other (OTH)

AF:

0.639

AC:

1349

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1854

3708

5561

7415

9269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.633

Hom.:

21922

Bravo

AF:

0.616

Asia WGS

AF:

0.625

AC:

2175

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.1

(source)

DANN

Benign

0.34

PhyloP100

-0.96

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