dbSNP rs451066: ENSG00000289583:n.138-13949C>T (chr14-68758968-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 ENST00000768252.1(ENSG00000289583):n.138-13949C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,016 control chromosomes in the GnomAD database, including 2,593 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 0.17 ( 2593 hom., cov: 32)

Consequence

ENSG00000289583
ENST00000768252.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206

Publications

7 publications found

Variant links:

Genes affected

ENSG00000289583 (HGNC:):

ENSG00000289583 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289583	ENST00000768252.1 link	n.138-13949C>T	intron_variant	Intron 1 of 3
ENSG00000289583	ENST00000768253.1 link	n.246+8778C>T	intron_variant	Intron 2 of 3
ENSG00000289583	ENST00000768254.1 link	n.233+8778C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25307

AN:

151898

Hom.:

2595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0683

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.172

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

GnomAD4 genome

AF:

0.167

AC:

25316

AN:

152016

Hom.:

2593

Cov.:

AF XY:

0.164

AC XY:

12225

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.0682

AC:

2828

AN:

41478

American (AMR)

AF:

0.274

AC:

4179

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

723

AN:

3470

East Asian (EAS)

AF:

0.150

AC:

773

AN:

5150

South Asian (SAS)

AF:

0.170

AC:

818

AN:

4810

European-Finnish (FIN)

AF:

0.117

AC:

1242

AN:

10586

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.208

AC:

14104

AN:

67944

Other (OTH)

AF:

0.169

AC:

355

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1022

2044

3067

4089

5111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.183

Hom.:

831

Bravo

AF:

0.180

Asia WGS

AF:

0.149

AC:

516

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.7

(source)

DANN

Benign

0.36

PhyloP100

0.21

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