Genetic Variant LOC107984625:n.234-10582A>G (chr13-59541970-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_001749886.2(LOC107984625):n.234-10582A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,156 control chromosomes in the GnomAD database, including 47,793 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 0.74 ( 47793 hom., cov: 32)

Consequence

LOC107984625
XR_001749886.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0820

Publications

3 publications found

Variant links:

Genes affected

LOC107984625 (HGNC:):

LOC107984625 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984625	XR_001749886.2 link	n.234-10582A>G		intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.737

AC:

112016

AN:

152038

Hom.:

47784

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.875

Gnomad AMR

AF:

0.843

Gnomad ASJ

AF:

0.858

Gnomad EAS

AF:

0.792

Gnomad SAS

AF:

0.890

Gnomad FIN

AF:

0.916

Gnomad MID

AF:

0.845

Gnomad NFE

AF:

0.944

Gnomad OTH

AF:

0.770

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

GnomAD4 genome

AF:

0.736

AC:

112033

AN:

152156

Hom.:

47793

Cov.:

AF XY:

0.740

AC XY:

55035

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.270

AC:

11181

AN:

41468

American (AMR)

AF:

0.843

AC:

12893

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.858

AC:

2977

AN:

3470

East Asian (EAS)

AF:

0.792

AC:

4094

AN:

5166

South Asian (SAS)

AF:

0.890

AC:

4287

AN:

4818

European-Finnish (FIN)

AF:

0.916

AC:

9715

AN:

10608

Middle Eastern (MID)

AF:

0.847

AC:

249

AN:

294

European-Non Finnish (NFE)

AF:

0.944

AC:

64205

AN:

68008

Other (OTH)

AF:

0.772

AC:

1634

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

853

1705

2558

3410

4263

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

786

1572

2358

3144

3930

<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:

0.880

Hom.:

100534

Bravo

AF:

0.710

Asia WGS

AF:

0.798

AC:

2778

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.81

(source)

DANN

Benign

0.58

PhyloP100

-0.082

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