Genetic Variant ENSG00000227240:n.378+118615A>G (chr1-194017982-A-G) – 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.378+118615A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.977 in 151,470 control chromosomes in the GnomAD database, including 72,373 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 0.98 ( 72373 hom., cov: 27)

Consequence

ENSG00000227240
ENST00000656143.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06

Publications

0 publications found

Variant links:

Genes affected

ENSG00000227240 (HGNC:):

ENSG00000227240 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 (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904475	XR_007066777.1 link	n.5413-108158A>G		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.2 link	n.378+118615A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.977

AC:

147871

AN:

151358

Hom.:

72324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.922

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.993

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

0.998

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

0.998

Gnomad OTH

AF:

0.987

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

GnomAD4 genome

AF:

0.977

AC:

147976

AN:

151470

Hom.:

72373

Cov.:

AF XY:

0.978

AC XY:

72363

AN XY:

74018

show subpopulations

African (AFR)

AF:

0.922

AC:

38080

AN:

41294

American (AMR)

AF:

0.993

AC:

15089

AN:

15198

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

3460

AN:

3460

East Asian (EAS)

AF:

1.00

AC:

5118

AN:

5118

South Asian (SAS)

AF:

1.00

AC:

4785

AN:

4786

European-Finnish (FIN)

AF:

0.998

AC:

10557

AN:

10574

Middle Eastern (MID)

AF:

0.983

AC:

289

AN:

294

European-Non Finnish (NFE)

AF:

0.998

AC:

67624

AN:

67744

Other (OTH)

AF:

0.987

AC:

2063

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

148

297

445

594

742

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.984

Hom.:

7347

Bravo

AF:

0.973

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.62

(source)

DANN

Benign

0.42

PhyloP100

-2.1

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