dbSNP rs11073059: ENSG00000294065:n.235-21840A>T (chr15-34697473-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000720751.1(ENSG00000294065):n.235-21840A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,050 control chromosomes in the GnomAD database, including 12,826 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 0.41 ( 12826 hom., cov: 33)

Consequence

ENSG00000294065
ENST00000720751.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.860

Publications

8 publications found

Variant links:

Genes affected

ENSG00000294065 (HGNC:):

ENSG00000294065 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=-0.97).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 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
ENSG00000294065	ENST00000720751.1 link	n.235-21840A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.408

AC:

62058

AN:

151932

Hom.:

12822

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.347

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.403

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

GnomAD4 genome

AF:

0.408

AC:

62093

AN:

152050

Hom.:

12826

Cov.:

AF XY:

0.407

AC XY:

30243

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.378

AC:

15693

AN:

41480

American (AMR)

AF:

0.373

AC:

5693

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

1196

AN:

3472

East Asian (EAS)

AF:

0.440

AC:

2276

AN:

5174

South Asian (SAS)

AF:

0.589

AC:

2839

AN:

4818

European-Finnish (FIN)

AF:

0.347

AC:

3662

AN:

10562

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.430

AC:

29204

AN:

67954

Other (OTH)

AF:

0.405

AC:

853

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1894

3787

5681

7574

9468

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

602

1204

1806

2408

3010

<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:

0.405

Hom.:

1569

Bravo

AF:

0.405

Asia WGS

AF:

0.515

AC:

1792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.65

(source)

DANN

Benign

0.37

PhyloP100

-0.86

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