dbSNP rs7098209: ENSG00000303320:n.1220-3347A>G (chr10-93715713-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000793614.1(ENSG00000303320):n.1220-3347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,128 control chromosomes in the GnomAD database, including 4,725 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 0.23 ( 4725 hom., cov: 32)

Consequence

ENSG00000303320
ENST00000793614.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.649

Publications

5 publications found

Variant links:

Genes affected

ENSG00000303320 (HGNC:):

ENSG00000303320 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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
ENSG00000303320	ENST00000793614.1 link	n.1220-3347A>G		intron_variant	Intron 3 of 3
ENSG00000303320	ENST00000793615.1 link	n.303-3347A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35355

AN:

152010

Hom.:

4709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.231

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

GnomAD4 genome

AF:

0.233

AC:

35397

AN:

152128

Hom.:

4725

Cov.:

AF XY:

0.228

AC XY:

16993

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.356

AC:

14746

AN:

41474

American (AMR)

AF:

0.177

AC:

2704

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

720

AN:

3468

East Asian (EAS)

AF:

0.275

AC:

1425

AN:

5174

South Asian (SAS)

AF:

0.249

AC:

1199

AN:

4822

European-Finnish (FIN)

AF:

0.142

AC:

1504

AN:

10600

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.180

AC:

12266

AN:

67988

Other (OTH)

AF:

0.234

AC:

493

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1361

2721

4082

5442

6803

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.201

Hom.:

9407

Bravo

AF:

0.238

Asia WGS

AF:

0.262

AC:

910

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.2

(source)

DANN

Benign

0.71

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