dbSNP rs10990136: ENSG00000289079:n.172+1197C>T (chr9-102496554-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 ENST00000692021.2(ENSG00000289079):n.172+1197C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,078 control chromosomes in the GnomAD database, including 329 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 0.058 ( 329 hom., cov: 32)

Consequence

ENSG00000289079
ENST00000692021.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.55

Publications

3 publications found

Variant links:

Genes affected

ENSG00000289079 (HGNC:):

ENSG00000289079 links:

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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 (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289079	ENST00000692021.2 link	n.172+1197C>T	intron_variant	Intron 1 of 2
ENSG00000289079	ENST00000731645.1 link	n.131+1197C>T	intron_variant	Intron 1 of 3
ENSG00000289079	ENST00000731646.1 link	n.287+6826C>T	intron_variant	Intron 3 of 3
ENSG00000289079	ENST00000731647.1 link	n.369+6826C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0579

AC:

8803

AN:

151960

Hom.:

328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0139

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0853

Gnomad ASJ

AF:

0.0305

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.0715

Gnomad FIN

AF:

0.0799

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0674

Gnomad OTH

AF:

0.0497

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

GnomAD4 genome

AF:

0.0579

AC:

8808

AN:

152078

Hom.:

329

Cov.:

AF XY:

0.0605

AC XY:

4497

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0139

AC:

576

AN:

41474

American (AMR)

AF:

0.0859

AC:

1312

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0305

AC:

106

AN:

3472

East Asian (EAS)

AF:

0.178

AC:

922

AN:

5170

South Asian (SAS)

AF:

0.0720

AC:

347

AN:

4820

European-Finnish (FIN)

AF:

0.0799

AC:

844

AN:

10564

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0674

AC:

4582

AN:

67980

Other (OTH)

AF:

0.0487

AC:

103

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

422

843

1265

1686

2108

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.0616

Hom.:

Bravo

AF:

0.0559

Asia WGS

AF:

0.0980

AC:

338

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

0.26

(source)

DANN

Benign

0.33

PhyloP100

-1.5

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