Genetic Variant ENSG00000227240:n.154-17107G>C (chr1-193656103-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 ENST00000656143.2(ENSG00000227240):n.154-17107G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,102 control chromosomes in the GnomAD database, including 2,615 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 0.18 ( 2615 hom., cov: 32)

Consequence

ENSG00000227240
ENST00000656143.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610

Publications

9 publications found

Variant links:

Genes affected

ENSG00000227240 (HGNC:):

ENSG00000227240 links:

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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 (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904475	XR_007066777.1 link	n.5234+182727G>C		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.2 link	n.154-17107G>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27303

AN:

151984

Hom.:

2612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.0256

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.178

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

GnomAD4 genome

AF:

0.180

AC:

27324

AN:

152102

Hom.:

2615

Cov.:

AF XY:

0.178

AC XY:

13227

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.205

AC:

8505

AN:

41488

American (AMR)

AF:

0.125

AC:

1910

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.190

AC:

661

AN:

3472

East Asian (EAS)

AF:

0.0257

AC:

133

AN:

5178

South Asian (SAS)

AF:

0.212

AC:

1025

AN:

4826

European-Finnish (FIN)

AF:

0.197

AC:

2076

AN:

10556

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.182

AC:

12390

AN:

67988

Other (OTH)

AF:

0.182

AC:

385

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1147

2293

3440

4586

5733

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.0985

Hom.:

167

Bravo

AF:

0.171

Asia WGS

AF:

0.137

AC:

477

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

1.3

(source)

DANN

Benign

0.42

PhyloP100

0.061

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