dbSNP rs7571001: ENSG00000222000:n.398+280A>G (chr2-98332937-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 ENST00000409490.6(ENSG00000222000):n.398+280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,074 control chromosomes in the GnomAD database, including 7,425 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 0.31 ( 7425 hom., cov: 32)

Consequence

ENSG00000222000
ENST00000409490.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.442

Publications

4 publications found

Variant links:

Genes affected

ENSG00000222000 (HGNC:):

ENSG00000222000 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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000222000	ENST00000409490.6 link	n.398+280A>G	intron_variant	Intron 3 of 3	4
ENSG00000222000	ENST00000467398.3 link	n.546+280A>G	intron_variant	Intron 2 of 2	4
ENSG00000222000	ENST00000731073.1 link	n.282+986A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.307

AC:

46632

AN:

151956

Hom.:

7402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.327

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

GnomAD4 genome

AF:

0.307

AC:

46718

AN:

152074

Hom.:

7425

Cov.:

AF XY:

0.300

AC XY:

22313

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.343

AC:

14234

AN:

41472

American (AMR)

AF:

0.373

AC:

5698

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

956

AN:

3466

East Asian (EAS)

AF:

0.189

AC:

981

AN:

5186

South Asian (SAS)

AF:

0.189

AC:

914

AN:

4824

European-Finnish (FIN)

AF:

0.178

AC:

1883

AN:

10578

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.310

AC:

21088

AN:

67958

Other (OTH)

AF:

0.324

AC:

682

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1594

3188

4783

6377

7971

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.317

Hom.:

24306

Bravo

AF:

0.327

Asia WGS

AF:

0.187

AC:

651

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.18

(source)

DANN

Benign

0.51

PhyloP100

-0.44

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