dbSNP rs6969802: ENSG00000304714:n.231+4675A>G (chr7-113009359-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000805775.1(ENSG00000304714):n.231+4675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,182 control chromosomes in the GnomAD database, including 1,896 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 0.13 ( 1896 hom., cov: 31)

Consequence

ENSG00000304714
ENST00000805775.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.973

Publications

2 publications found

Variant links:

Genes affected

ENSG00000304714 (HGNC:):

ENSG00000304714 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 (AFR) allele frequency at 95% confidence interval = 0.254 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
ENSG00000304714	ENST00000805775.1 link	n.231+4675A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20341

AN:

152064

Hom.:

1894

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0910

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.0613

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0863

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.134

AC:

20363

AN:

152182

Hom.:

1896

Cov.:

AF XY:

0.130

AC XY:

9687

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.258

AC:

10690

AN:

41482

American (AMR)

AF:

0.108

AC:

1654

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0910

AC:

316

AN:

3472

East Asian (EAS)

AF:

0.00116

AC:

AN:

5180

South Asian (SAS)

AF:

0.158

AC:

762

AN:

4824

European-Finnish (FIN)

AF:

0.0613

AC:

650

AN:

10606

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0863

AC:

5870

AN:

68006

Other (OTH)

AF:

0.117

AC:

248

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

831

1662

2494

3325

4156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.114

Hom.:

164

Bravo

AF:

0.142

Asia WGS

AF:

0.0830

AC:

289

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

8.4

(source)

DANN

Benign

0.66

PhyloP100

0.97

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