dbSNP rs11772451: ENSG00000227489:n.306+357G>C (chr7-15066869-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000445093.1(ENSG00000227489):n.306+357G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,728 control chromosomes in the GnomAD database, including 14,816 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 0.39 ( 14816 hom., cov: 32)

Consequence

ENSG00000227489
ENST00000445093.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

3 publications found

Variant links:

Genes affected

ENSG00000227489 (HGNC:):

ENSG00000227489 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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 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
ENSG00000227489	ENST00000445093.1 link	n.306+357G>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.390

AC:

59123

AN:

151610

Hom.:

14771

Cov.:

show subpopulations

Gnomad AFR

AF:

0.694

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.558

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.334

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

GnomAD4 genome

AF:

0.390

AC:

59218

AN:

151728

Hom.:

14816

Cov.:

AF XY:

0.394

AC XY:

29182

AN XY:

74160

show subpopulations

African (AFR)

AF:

0.695

AC:

28766

AN:

41400

American (AMR)

AF:

0.380

AC:

5791

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

606

AN:

3462

East Asian (EAS)

AF:

0.558

AC:

2867

AN:

5142

South Asian (SAS)

AF:

0.257

AC:

1234

AN:

4798

European-Finnish (FIN)

AF:

0.304

AC:

3201

AN:

10540

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.233

AC:

15831

AN:

67860

Other (OTH)

AF:

0.335

AC:

704

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1535

3069

4604

6138

7673

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

518

1036

1554

2072

2590

<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:

0.173

Hom.:

381

Bravo

AF:

0.413

Asia WGS

AF:

0.429

AC:

1486

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.23

(source)

DANN

Benign

0.38

PhyloP100

-1.1

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