Genetic Variant LOC105377725:n.3056-1803T>A (chr5-171797539-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001742985.3(LOC105377725):n.3056-1803T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 152,294 control chromosomes in the GnomAD database, including 1,684 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 0.092 ( 1684 hom., cov: 33)

Consequence

LOC105377725
XR_001742985.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.686

Publications

1 publications found

Variant links:

Genes affected

LOC105377725 (HGNC:):

LOC105377725 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105377725	XR_001742985.3 link	n.3056-1803T>A	intron_variant	Intron 2 of 3
LOC105377725	XR_007059049.1 link	n.2773-645T>A	intron_variant	Intron 2 of 2
LOC105377725	XR_007059050.1 link	n.2773-645T>A	intron_variant	Intron 2 of 3
LOC105377725	XR_007059051.1 link	n.633-645T>A	intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0920

AC:

13999

AN:

152174

Hom.:

1665

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0446

Gnomad ASJ

AF:

0.00720

Gnomad EAS

AF:

0.0152

Gnomad SAS

AF:

0.0509

Gnomad FIN

AF:

0.0151

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0117

Gnomad OTH

AF:

0.0793

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

GnomAD4 genome

AF:

0.0923

AC:

14050

AN:

152294

Hom.:

1684

Cov.:

AF XY:

0.0905

AC XY:

6739

AN XY:

74504

show subpopulations

African (AFR)

AF:

0.286

AC:

11880

AN:

41510

American (AMR)

AF:

0.0446

AC:

682

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00720

AC:

AN:

3472

East Asian (EAS)

AF:

0.0152

AC:

AN:

5192

South Asian (SAS)

AF:

0.0501

AC:

242

AN:

4830

European-Finnish (FIN)

AF:

0.0151

AC:

160

AN:

10630

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0117

AC:

798

AN:

68042

Other (OTH)

AF:

0.0804

AC:

170

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

549

1099

1648

2198

2747

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0168

Hom.:

Bravo

AF:

0.102

Asia WGS

AF:

0.0610

AC:

213

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.71

(source)

DANN

Benign

0.89

PhyloP100

-0.69

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