Genetic Variant ENSG00000289097:n.722-29971G>A (chr6-18352925-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 ENST00000790360.1(ENSG00000289097):n.722-29971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,010 control chromosomes in the GnomAD database, including 7,772 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 0.31 ( 7772 hom., cov: 32)

Consequence

ENSG00000289097
ENST00000790360.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.842

Publications

7 publications found

Variant links:

Genes affected

ENSG00000289097 (HGNC:):

ENSG00000289097 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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
ENSG00000289097	ENST00000790360.1 link	n.722-29971G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47380

AN:

151892

Hom.:

7769

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.363

Gnomad OTH

AF:

0.326

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

GnomAD4 genome

AF:

0.312

AC:

47395

AN:

152010

Hom.:

7772

Cov.:

AF XY:

0.311

AC XY:

23114

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.221

AC:

9181

AN:

41452

American (AMR)

AF:

0.254

AC:

3879

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1230

AN:

3468

East Asian (EAS)

AF:

0.416

AC:

2149

AN:

5164

South Asian (SAS)

AF:

0.232

AC:

1118

AN:

4822

European-Finnish (FIN)

AF:

0.367

AC:

3864

AN:

10536

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.363

AC:

24684

AN:

67990

Other (OTH)

AF:

0.326

AC:

690

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1681

3361

5042

6722

8403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.340

Hom.:

3587

Bravo

AF:

0.302

Asia WGS

AF:

0.329

AC:

1139

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

0.73

PhyloP100

0.84

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