dbSNP rs298157: ENSG00000303463:n.393-12721G>A (chr1-60406619-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 ENST00000794751.1(ENSG00000303463):n.393-12721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0854 in 152,096 control chromosomes in the GnomAD database, including 595 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 0.085 ( 595 hom., cov: 32)

Consequence

ENSG00000303463
ENST00000794751.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650

Publications

1 publications found

Variant links:

Genes affected

ENSG00000303463 (HGNC:):

ENSG00000303463 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=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303463	ENST00000794751.1 link	n.393-12721G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0854

AC:

12982

AN:

151980

Hom.:

596

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0726

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.0656

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0880

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0971

Gnomad OTH

AF:

0.0851

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

GnomAD4 genome

AF:

0.0854

AC:

12986

AN:

152096

Hom.:

595

Cov.:

AF XY:

0.0860

AC XY:

6396

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.0726

AC:

3012

AN:

41490

American (AMR)

AF:

0.0655

AC:

1001

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

534

AN:

3466

East Asian (EAS)

AF:

0.00193

AC:

AN:

5168

South Asian (SAS)

AF:

0.123

AC:

594

AN:

4814

European-Finnish (FIN)

AF:

0.0880

AC:

933

AN:

10600

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0972

AC:

6605

AN:

67964

Other (OTH)

AF:

0.0837

AC:

177

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

600

1199

1799

2398

2998

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<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:

0.102

Hom.:

380

Bravo

AF:

0.0819

Asia WGS

AF:

0.0580

AC:

202

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.77

(source)

DANN

Benign

0.21

PhyloP100

-0.65

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