Genetic Variant ENSG00000229321:n.348-9236G>A (chr2-206854160-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 ENST00000438070.3(ENSG00000229321):n.348-9236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,060 control chromosomes in the GnomAD database, including 983 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 0.11 ( 983 hom., cov: 32)

Consequence

ENSG00000229321
ENST00000438070.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158

Publications

2 publications found

Variant links:

Genes affected

ENSG00000229321 (HGNC:):

ENSG00000229321 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000229321	ENST00000438070.3 link	n.348-9236G>A	intron_variant	Intron 2 of 6	3
ENSG00000229321	ENST00000658291.1 link	n.3035-9236G>A	intron_variant	Intron 2 of 3
ENSG00000229321	ENST00000658889.1 link	n.2974-25223G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16850

AN:

151942

Hom.:

980

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0970

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.0880

Gnomad MID

AF:

0.0796

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.111

AC:

16860

AN:

152060

Hom.:

983

Cov.:

AF XY:

0.109

AC XY:

8126

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.129

AC:

5361

AN:

41466

American (AMR)

AF:

0.0971

AC:

1484

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

395

AN:

3470

East Asian (EAS)

AF:

0.109

AC:

566

AN:

5178

South Asian (SAS)

AF:

0.115

AC:

554

AN:

4820

European-Finnish (FIN)

AF:

0.0880

AC:

929

AN:

10552

Middle Eastern (MID)

AF:

0.0753

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.107

AC:

7252

AN:

67978

Other (OTH)

AF:

0.117

AC:

247

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

759

1519

2278

3038

3797

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.0930

Hom.:

354

Bravo

AF:

0.111

Asia WGS

AF:

0.110

AC:

386

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.8

(source)

DANN

Benign

0.51

PhyloP100

0.16

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