dbSNP rs12708283: LOC105376214:n.721-61300G>A (chr9-108114594-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_001746881.2(LOC105376214):n.721-61300G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,910 control chromosomes in the GnomAD database, including 5,554 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 0.26 ( 5554 hom., cov: 31)

Consequence

LOC105376214
XR_001746881.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.442

Publications

0 publications found

Variant links:

Genes affected

LOC105376214 (HGNC:):

LOC105376214 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 (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376214	XR_001746881.2 link	n.721-61300G>A	intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2 link	n.721-61300G>A	intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1 link	n.721-61300G>A	intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39814

AN:

151794

Hom.:

5553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.0196

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.290

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

GnomAD4 genome

AF:

0.262

AC:

39826

AN:

151910

Hom.:

5554

Cov.:

AF XY:

0.258

AC XY:

19148

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.244

AC:

10108

AN:

41382

American (AMR)

AF:

0.261

AC:

3979

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

652

AN:

3466

East Asian (EAS)

AF:

0.0193

AC:

100

AN:

5184

South Asian (SAS)

AF:

0.189

AC:

908

AN:

4802

European-Finnish (FIN)

AF:

0.289

AC:

3044

AN:

10550

Middle Eastern (MID)

AF:

0.315

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.292

AC:

19851

AN:

67948

Other (OTH)

AF:

0.285

AC:

601

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1477

2954

4432

5909

7386

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.274

Hom.:

1193

Bravo

AF:

0.263

Asia WGS

AF:

0.124

AC:

432

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

6.1

(source)

DANN

Benign

0.55

PhyloP100

0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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