dbSNP rs1992788: ENSG00000289349:n.464-30236G>T (chr2-175802375-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000685522.2(ENSG00000289349):n.464-30236G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,014 control chromosomes in the GnomAD database, including 4,566 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 0.24 ( 4566 hom., cov: 32)

Consequence

ENSG00000289349
ENST00000685522.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0320

Publications

1 publications found

Variant links:

Genes affected

ENSG00000289349 (HGNC:):

ENSG00000289349 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 (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985962	XR_007087312.1 link	n.150-16599C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289349	ENST00000685522.2 link	n.464-30236G>T	intron_variant	Intron 1 of 2
ENSG00000289349	ENST00000692740.2 link	n.326-30236G>T	intron_variant	Intron 2 of 3
ENSG00000289349	ENST00000840653.1 link	n.272-30236G>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36293

AN:

151896

Hom.:

4563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.186

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.261

Gnomad OTH

AF:

0.264

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

GnomAD4 genome

AF:

0.239

AC:

36334

AN:

152014

Hom.:

4566

Cov.:

AF XY:

0.243

AC XY:

18066

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.188

AC:

7810

AN:

41490

American (AMR)

AF:

0.200

AC:

3054

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1021

AN:

3468

East Asian (EAS)

AF:

0.186

AC:

962

AN:

5162

South Asian (SAS)

AF:

0.367

AC:

1769

AN:

4820

European-Finnish (FIN)

AF:

0.307

AC:

3225

AN:

10520

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.261

AC:

17750

AN:

67960

Other (OTH)

AF:

0.265

AC:

561

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1409

2818

4228

5637

7046

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.264

Hom.:

2973

Bravo

AF:

0.229

Asia WGS

AF:

0.237

AC:

822

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

2.1

(source)

DANN

Benign

0.55

PhyloP100

-0.032

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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