Genetic Variant ENSG00000309216:n.407-5456G>A (chr2-224620019-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 ENST00000839568.1(ENSG00000309216):n.407-5456G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,922 control chromosomes in the GnomAD database, including 18,209 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 0.49 ( 18209 hom., cov: 33)

Consequence

ENSG00000309216
ENST00000839568.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Publications

3 publications found

Variant links:

Genes affected

ENSG00000309216 (HGNC:):

ENSG00000309216 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373909	XR_923955.1 link	n.214+12701G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309216	ENST00000839568.1 link	n.407-5456G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.488

AC:

74072

AN:

151804

Hom.:

18215

Cov.:

show subpopulations

Gnomad AFR

AF:

0.478

Gnomad AMI

AF:

0.565

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.374

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.490

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.493

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

GnomAD4 genome

AF:

0.488

AC:

74100

AN:

151922

Hom.:

18209

Cov.:

AF XY:

0.482

AC XY:

35819

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.478

AC:

19796

AN:

41428

American (AMR)

AF:

0.408

AC:

6222

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.504

AC:

1748

AN:

3470

East Asian (EAS)

AF:

0.372

AC:

1927

AN:

5174

South Asian (SAS)

AF:

0.483

AC:

2328

AN:

4822

European-Finnish (FIN)

AF:

0.490

AC:

5148

AN:

10504

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.519

AC:

35239

AN:

67952

Other (OTH)

AF:

0.490

AC:

1034

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1961

3922

5883

7844

9805

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

676

1352

2028

2704

3380

<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:

0.502

Hom.:

56100

Bravo

AF:

0.478

Asia WGS

AF:

0.410

AC:

1424

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.8

(source)

DANN

Benign

0.49

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