dbSNP rs28954369: ENSG00000289434:n.169-17851G>A (chr7-128239391-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000785131.1(ENSG00000289434):n.169-17851G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,138 control chromosomes in the GnomAD database, including 582 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 0.070 ( 582 hom., cov: 32)

Consequence

ENSG00000289434
ENST00000785131.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.938

Publications

4 publications found

Variant links:

Genes affected

ENSG00000289434 (HGNC:):

ENSG00000289434 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 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
ENSG00000289434	ENST00000785131.1 link	n.169-17851G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0696

AC:

10579

AN:

152018

Hom.:

582

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0170

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0423

Gnomad ASJ

AF:

0.0219

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0218

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.0483

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

GnomAD4 genome

AF:

0.0695

AC:

10578

AN:

152138

Hom.:

582

Cov.:

AF XY:

0.0706

AC XY:

5247

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0169

AC:

703

AN:

41512

American (AMR)

AF:

0.0422

AC:

646

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0219

AC:

AN:

3470

East Asian (EAS)

AF:

0.000967

AC:

AN:

5170

South Asian (SAS)

AF:

0.0220

AC:

106

AN:

4820

European-Finnish (FIN)

AF:

0.183

AC:

1937

AN:

10558

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.103

AC:

6971

AN:

67994

Other (OTH)

AF:

0.0477

AC:

101

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

475

949

1424

1898

2373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0889

Hom.:

Bravo

AF:

0.0555

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.5

(source)

DANN

Benign

0.68

PhyloP100

-0.94

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