dbSNP rs954368: ENSG00000280241:n.405+8357T>C (chr4-153850624-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000839747.1(ENSG00000280241):n.405+8357T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,096 control chromosomes in the GnomAD database, including 935 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 0.10 ( 935 hom., cov: 31)

Consequence

ENSG00000280241
ENST00000839747.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379

Publications

8 publications found

Variant links:

Genes affected

ENSG00000280241 (HGNC:):

ENSG00000280241 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 (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927947	XR_007058336.1 link	n.3440+8357T>C		intron_variant	Intron 3 of 14

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000280241	ENST00000839747.1 link	n.405+8357T>C	intron_variant	Intron 3 of 8
ENSG00000280241	ENST00000839748.1 link	n.505+8357T>C	intron_variant	Intron 3 of 6
ENSG00000280241	ENST00000839749.1 link	n.200-33335T>C	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15206

AN:

151978

Hom.:

931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0563

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.0582

Gnomad ASJ

AF:

0.0819

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.0863

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

GnomAD4 genome

AF:

0.100

AC:

15220

AN:

152096

Hom.:

935

Cov.:

AF XY:

0.101

AC XY:

7534

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0565

AC:

2344

AN:

41510

American (AMR)

AF:

0.0580

AC:

886

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0819

AC:

284

AN:

3466

East Asian (EAS)

AF:

0.146

AC:

754

AN:

5162

South Asian (SAS)

AF:

0.269

AC:

1290

AN:

4796

European-Finnish (FIN)

AF:

0.110

AC:

1166

AN:

10582

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.119

AC:

8110

AN:

67996

Other (OTH)

AF:

0.0892

AC:

188

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

704

1407

2111

2814

3518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.108

Hom.:

1876

Bravo

AF:

0.0889

Asia WGS

AF:

0.178

AC:

618

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

(source)

DANN

Benign

0.63

PhyloP100

-0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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