dbSNP rs7318572: ENSG00000296879:n.228+3293A>T (chr13-23104796-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 ENST00000743290.1(ENSG00000296879):n.228+3293A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 152,256 control chromosomes in the GnomAD database, including 400 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 0.052 ( 400 hom., cov: 32)

Consequence

ENSG00000296879
ENST00000743290.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.528

Publications

2 publications found

Variant links:

Genes affected

ENSG00000296879 (HGNC:):

ENSG00000296879 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 (EAS) allele frequency at 95% confidence interval = 0.144 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
ENSG00000296879	ENST00000743290.1 link	n.228+3293A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0515

AC:

7832

AN:

152138

Hom.:

395

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0188

Gnomad ASJ

AF:

0.0225

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0159

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0189

Gnomad OTH

AF:

0.0310

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

GnomAD4 genome

AF:

0.0516

AC:

7861

AN:

152256

Hom.:

400

Cov.:

AF XY:

0.0534

AC XY:

3972

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.113

AC:

4677

AN:

41530

American (AMR)

AF:

0.0188

AC:

288

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0225

AC:

AN:

3472

East Asian (EAS)

AF:

0.153

AC:

792

AN:

5170

South Asian (SAS)

AF:

0.102

AC:

493

AN:

4816

European-Finnish (FIN)

AF:

0.0159

AC:

169

AN:

10612

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0189

AC:

1287

AN:

68034

Other (OTH)

AF:

0.0345

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

369

738

1108

1477

1846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<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:

0.0361

Hom.:

Bravo

AF:

0.0528

Asia WGS

AF:

0.115

AC:

400

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

1.0

(source)

DANN

Benign

0.66

PhyloP100

-0.53

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