dbSNP rs7335200: ENSG00000296879:n.229-783C>T (chr13-23083379-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 ENST00000743290.1(ENSG00000296879):n.229-783C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,102 control chromosomes in the GnomAD database, including 1,442 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 0.14 ( 1442 hom., cov: 32)

Consequence

ENSG00000296879
ENST00000743290.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700

Publications

5 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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.229-783C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20540

AN:

151984

Hom.:

1432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.0892

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

AF:

0.135

AC:

20573

AN:

152102

Hom.:

1442

Cov.:

AF XY:

0.139

AC XY:

10319

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.161

AC:

6688

AN:

41494

American (AMR)

AF:

0.117

AC:

1782

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

564

AN:

3470

East Asian (EAS)

AF:

0.0896

AC:

464

AN:

5178

South Asian (SAS)

AF:

0.139

AC:

670

AN:

4820

European-Finnish (FIN)

AF:

0.191

AC:

2019

AN:

10548

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7898

AN:

68000

Other (OTH)

AF:

0.132

AC:

279

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

921

1842

2763

3684

4605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.121

Hom.:

1931

Bravo

AF:

0.132

Asia WGS

AF:

0.114

AC:

399

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.65

(source)

DANN

Benign

0.70

PhyloP100

0.0070

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