dbSNP rs11681243: ENSG00000230773:n.241-20592C>A (chr2-48024017-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000447571.5(ENSG00000230773):n.241-20592C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,116 control chromosomes in the GnomAD database, including 905 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 ( 905 hom., cov: 32)

Consequence

ENSG00000230773
ENST00000447571.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.338

Publications

4 publications found

Variant links:

Genes affected

ENSG00000230773 (HGNC:):

ENSG00000230773 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000230773	ENST00000447571.5 link	n.241-20592C>A	intron_variant	Intron 3 of 8	1
ENSG00000230773	ENST00000587616.1 link	n.191-1614C>A	intron_variant	Intron 2 of 10	5
ENSG00000230773	ENST00000649883.1 link	n.202-20592C>A	intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15378

AN:

151998

Hom.:

904

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0859

Gnomad AMI

AF:

0.0617

Gnomad AMR

AF:

0.0732

Gnomad ASJ

AF:

0.0407

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0162

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.0973

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

GnomAD4 genome

AF:

0.101

AC:

15390

AN:

152116

Hom.:

905

Cov.:

AF XY:

0.0993

AC XY:

7382

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.0859

AC:

3566

AN:

41496

American (AMR)

AF:

0.0731

AC:

1117

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0407

AC:

141

AN:

3464

East Asian (EAS)

AF:

0.000772

AC:

AN:

5184

South Asian (SAS)

AF:

0.0166

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.150

AC:

1585

AN:

10568

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.127

AC:

8635

AN:

67992

Other (OTH)

AF:

0.0958

AC:

202

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

686

1372

2059

2745

3431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<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:

0.110

Hom.:

169

Bravo

AF:

0.0945

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.75

(source)

DANN

Benign

0.82

PhyloP100

-0.34

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