Genetic Variant LOC105369657:n.31+914G>C (chr12-10536155-C-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_001749003.3(LOC105369657):n.31+914G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,598 control chromosomes in the GnomAD database, including 5,908 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 0.25 ( 5908 hom., cov: 32)

Consequence

LOC105369657
XR_001749003.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

Publications

2 publications found

Variant links:

Genes affected

LOC105369657 (HGNC:):

LOC105369657 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369657	XR_001749003.3 link	n.31+914G>C		intron_variant	Intron 1 of 4
LOC105369657	XR_931355.4 link	n.31+914G>C		intron_variant	Intron 1 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38499

AN:

151480

Hom.:

5891

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.690

Gnomad SAS

AF:

0.327

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.261

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

GnomAD4 genome

AF:

0.254

AC:

38532

AN:

151598

Hom.:

5908

Cov.:

AF XY:

0.260

AC XY:

19271

AN XY:

74046

show subpopulations

African (AFR)

AF:

0.125

AC:

5172

AN:

41388

American (AMR)

AF:

0.378

AC:

5755

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.301

AC:

1045

AN:

3466

East Asian (EAS)

AF:

0.690

AC:

3561

AN:

5162

South Asian (SAS)

AF:

0.326

AC:

1565

AN:

4804

European-Finnish (FIN)

AF:

0.254

AC:

2646

AN:

10412

Middle Eastern (MID)

AF:

0.226

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.265

AC:

17950

AN:

67834

Other (OTH)

AF:

0.268

AC:

565

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1380

2760

4141

5521

6901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.237

Hom.:

578

Bravo

AF:

0.263

Asia WGS

AF:

0.480

AC:

1669

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.4

(source)

DANN

Benign

0.37

PhyloP100

0.055

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