dbSNP rs10498919: ENSG00000230309:n.1038-34063C>G (chr6-78238016-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715178.1(ENSG00000230309):n.1038-34063C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 152,050 control chromosomes in the GnomAD database, including 750 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 0.045 ( 750 hom., cov: 32)

Consequence

ENSG00000230309
ENST00000715178.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0390

Publications

4 publications found

Variant links:

Genes affected

ENSG00000230309 (HGNC:):

ENSG00000230309 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377865	XR_002956359.2 link	n.135-34063C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1 link	n.1038-34063C>G		intron_variant	Intron 6 of 14

Frequencies

GnomAD3 genomes

AF:

0.0445

AC:

6759

AN:

151934

Hom.:

744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00853

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.182

Gnomad ASJ

AF:

0.00836

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.0559

Gnomad FIN

AF:

0.0999

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00624

Gnomad OTH

AF:

0.0484

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

GnomAD4 genome

AF:

0.0446

AC:

6776

AN:

152050

Hom.:

750

Cov.:

AF XY:

0.0527

AC XY:

3918

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.00850

AC:

353

AN:

41522

American (AMR)

AF:

0.183

AC:

2792

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.00836

AC:

AN:

3468

East Asian (EAS)

AF:

0.340

AC:

1752

AN:

5160

South Asian (SAS)

AF:

0.0551

AC:

265

AN:

4808

European-Finnish (FIN)

AF:

0.0999

AC:

1055

AN:

10556

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00624

AC:

424

AN:

67966

Other (OTH)

AF:

0.0502

AC:

106

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

259

518

777

1036

1295

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0285

Hom.:

Bravo

AF:

0.0557

Asia WGS

AF:

0.157

AC:

543

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.0

(source)

DANN

Benign

0.59

PhyloP100

0.039

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