dbSNP rs1695718: LOC105375716:n.559+63590G>A (chr8-117377370-C-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_007061067.1(LOC105375716):n.559+63590G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,774 control chromosomes in the GnomAD database, including 4,064 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 0.20 ( 4064 hom., cov: 32)

Consequence

LOC105375716
XR_007061067.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.309

Publications

1 publications found

Variant links:

Genes affected

LOC105375716 (HGNC:):

LOC105375716 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375716	XR_007061067.1 link	n.559+63590G>A	intron_variant	Intron 3 of 5
LOC105375716	XR_007061068.1 link	n.946+63590G>A	intron_variant	Intron 5 of 7
LOC105375716	XR_928568.4 link	n.714+63590G>A	intron_variant	Intron 4 of 6

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31105

AN:

151656

Hom.:

4065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0580

Gnomad AMI

AF:

0.277

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.197

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.198

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

GnomAD4 genome

AF:

0.205

AC:

31088

AN:

151774

Hom.:

4064

Cov.:

AF XY:

0.205

AC XY:

15194

AN XY:

74172

show subpopulations

African (AFR)

AF:

0.0579

AC:

2389

AN:

41296

American (AMR)

AF:

0.136

AC:

2073

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.227

AC:

788

AN:

3472

East Asian (EAS)

AF:

0.323

AC:

1660

AN:

5142

South Asian (SAS)

AF:

0.210

AC:

1011

AN:

4808

European-Finnish (FIN)

AF:

0.291

AC:

3068

AN:

10552

Middle Eastern (MID)

AF:

0.182

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.285

AC:

19384

AN:

67980

Other (OTH)

AF:

0.194

AC:

409

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1175

2350

3526

4701

5876

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.265

Hom.:

4922

Bravo

AF:

0.187

Asia WGS

AF:

0.214

AC:

744

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.3

(source)

DANN

Benign

0.63

PhyloP100

0.31

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