dbSNP rs10502519: LOC105372044:n.70-8297A>C (chr18-29245022-T-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_935327.3(LOC105372044):n.70-8297A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 152,260 control chromosomes in the GnomAD database, including 314 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 0.062 ( 314 hom., cov: 32)

Consequence

LOC105372044
XR_935327.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0840

Publications

1 publications found

Variant links:

Genes affected

LOC105372044 (HGNC:):

LOC105372044 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 (AMR) allele frequency at 95% confidence interval = 0.0917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372044	XR_935327.3 link	n.70-8297A>C		intron_variant	Intron 1 of 4
LOC105372044	XR_935328.2 link	n.61-8297A>C		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0615

AC:

9356

AN:

152142

Hom.:

314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0312

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.0954

Gnomad ASJ

AF:

0.0389

Gnomad EAS

AF:

0.0776

Gnomad SAS

AF:

0.0653

Gnomad FIN

AF:

0.0532

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0738

Gnomad OTH

AF:

0.0593

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

GnomAD4 genome

AF:

0.0616

AC:

9377

AN:

152260

Hom.:

314

Cov.:

AF XY:

0.0606

AC XY:

4510

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0313

AC:

1303

AN:

41564

American (AMR)

AF:

0.0958

AC:

1464

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0389

AC:

135

AN:

3470

East Asian (EAS)

AF:

0.0780

AC:

404

AN:

5180

South Asian (SAS)

AF:

0.0651

AC:

314

AN:

4822

European-Finnish (FIN)

AF:

0.0532

AC:

565

AN:

10616

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0738

AC:

5022

AN:

68004

Other (OTH)

AF:

0.0587

AC:

124

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

450

900

1350

1800

2250

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0633

Hom.:

Bravo

AF:

0.0632

Asia WGS

AF:

0.0570

AC:

199

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.2

(source)

DANN

Benign

0.68

PhyloP100

0.084

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