dbSNP rs7224319: ENSG00000306126:n.219+20528G>A (chr17-41001135-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000815517.1(ENSG00000306126):n.219+20528G>A 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 152,122 control chromosomes in the GnomAD database, including 6,929 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 ( 6929 hom., cov: 33)

Consequence

ENSG00000306126
ENST00000815517.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.588

Publications

2 publications found

Variant links:

Genes affected

ENSG00000306126 (HGNC:):

ENSG00000306126 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 = 0.528 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
ENSG00000306126	ENST00000815517.1 link	n.219+20528G>A		intron_variant	Intron 2 of 2
ENSG00000306126	ENST00000815518.1 link	n.159+20528G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35412

AN:

152004

Hom.:

6896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.533

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.0775

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0898

Gnomad OTH

AF:

0.205

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

GnomAD4 genome

AF:

0.233

AC:

35490

AN:

152122

Hom.:

6929

Cov.:

AF XY:

0.234

AC XY:

17378

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.534

AC:

22142

AN:

41450

American (AMR)

AF:

0.205

AC:

3128

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0775

AC:

269

AN:

3472

East Asian (EAS)

AF:

0.243

AC:

1259

AN:

5180

South Asian (SAS)

AF:

0.168

AC:

809

AN:

4816

European-Finnish (FIN)

AF:

0.120

AC:

1270

AN:

10580

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0898

AC:

6106

AN:

68012

Other (OTH)

AF:

0.203

AC:

429

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1119

2238

3356

4475

5594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.154

Hom.:

489

Bravo

AF:

0.256

Asia WGS

AF:

0.238

AC:

828

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.53

(source)

DANN

Benign

0.71

PhyloP100

-0.59

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