dbSNP rs9821892: ENSG00000285585:c.*1+22004A>T (chr3-119773102-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000648112.1(ENSG00000285585):c.*1+22004A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,710 control chromosomes in the GnomAD database, including 12,375 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 0.35 ( 12375 hom., cov: 32)

Consequence

ENSG00000285585
ENST00000648112.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.153

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285585 (HGNC:):

ENSG00000285585 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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
ENSG00000285585	ENST00000648112.1 link	c.*1+22004A>T		intron_variant	Intron 17 of 17			ENSP00000497876.1

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53533

AN:

151594

Hom.:

12344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.349

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

GnomAD4 genome

AF:

0.353

AC:

53611

AN:

151710

Hom.:

12375

Cov.:

AF XY:

0.352

AC XY:

26108

AN XY:

74114

show subpopulations

African (AFR)

AF:

0.665

AC:

27506

AN:

41346

American (AMR)

AF:

0.311

AC:

4742

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

795

AN:

3466

East Asian (EAS)

AF:

0.213

AC:

1098

AN:

5154

South Asian (SAS)

AF:

0.286

AC:

1374

AN:

4800

European-Finnish (FIN)

AF:

0.245

AC:

2561

AN:

10440

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.212

AC:

14418

AN:

67926

Other (OTH)

AF:

0.346

AC:

730

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1457

2914

4372

5829

7286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.318

Hom.:

931

Bravo

AF:

0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.4

(source)

DANN

Benign

0.54

PhyloP100

-0.15

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