dbSNP rs11045777: ENSG00000257062:n.*114+390G>A (chr12-21126647-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 ENST00000593147.5(ENSG00000257062):n.*114+390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,978 control chromosomes in the GnomAD database, including 2,066 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 0.15 ( 2066 hom., cov: 31)

Consequence

ENSG00000257062
ENST00000593147.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.472

Publications

5 publications found

Variant links:

COSMIC-nc: COSV57016556

Genes affected

ENSG00000257062 (HGNC:):

ENSG00000257062 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 (NFE) allele frequency at 95% confidence interval = 0.192 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
ENSG00000257062	ENST00000593147.5 link	n.*114+390G>A		intron_variant	Intron 5 of 5	5		ENSP00000467209.1		K7EP34

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23371

AN:

151860

Hom.:

2067

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.0715

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.168

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

GnomAD4 genome

AF:

0.154

AC:

23373

AN:

151978

Hom.:

2066

Cov.:

AF XY:

0.146

AC XY:

10874

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.114

AC:

4745

AN:

41476

American (AMR)

AF:

0.148

AC:

2253

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

871

AN:

3470

East Asian (EAS)

AF:

0.00193

AC:

AN:

5170

South Asian (SAS)

AF:

0.0718

AC:

346

AN:

4818

European-Finnish (FIN)

AF:

0.103

AC:

1094

AN:

10596

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.195

AC:

13226

AN:

67922

Other (OTH)

AF:

0.165

AC:

348

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

971

1942

2912

3883

4854

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.184

Hom.:

3961

Bravo

AF:

0.158

Asia WGS

AF:

0.0400

AC:

140

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

1.7

(source)

DANN

Benign

0.49

PhyloP100

-0.47

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