dbSNP rs3829210: ENSG00000297096:n.539+2296G>A (chr8-131041906-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 ENST00000745365.1(ENSG00000297096):n.539+2296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,178 control chromosomes in the GnomAD database, including 15,737 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 0.44 ( 15732 hom., cov: 34)

Exomes 𝑓: 0.47 ( 5 hom. )

Consequence

ENSG00000297096
ENST00000745365.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Publications

4 publications found

Variant links:

Genes affected

ENSG00000297096 (HGNC:):

ENSG00000297096 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=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375760	XR_007061182.1 link	n.89+2296G>A	intron_variant	Intron 1 of 3
LOC105375760	XR_007061183.1 link	n.89+2296G>A	intron_variant	Intron 1 of 5
LOC105375760	XR_928653.3 link	n.81+2296G>A	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297096	ENST00000745365.1 link	n.539+2296G>A	intron_variant	Intron 1 of 3
ENSG00000297096	ENST00000745366.1 link	n.98+2296G>A	intron_variant	Intron 1 of 5
ENSG00000297096	ENST00000745367.1 link	n.99+1491G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67651

AN:

152024

Hom.:

15733

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.339

Gnomad AMR

AF:

0.479

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.633

Gnomad SAS

AF:

0.546

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.448

GnomAD4 exome

AF:

0.472

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.467

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.445

AC:

67671

AN:

152142

Hom.:

15732

Cov.:

AF XY:

0.452

AC XY:

33635

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.307

AC:

12761

AN:

41524

American (AMR)

AF:

0.479

AC:

7323

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1490

AN:

3470

East Asian (EAS)

AF:

0.632

AC:

3248

AN:

5136

South Asian (SAS)

AF:

0.547

AC:

2641

AN:

4824

European-Finnish (FIN)

AF:

0.527

AC:

5592

AN:

10608

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.489

AC:

33222

AN:

67970

Other (OTH)

AF:

0.450

AC:

951

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1929

3859

5788

7718

9647

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.480

Hom.:

35690

Bravo

AF:

0.432

Asia WGS

AF:

0.570

AC:

1982

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

3.8

(source)

DANN

Benign

0.93

PhyloP100

-0.23

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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