Genetic Variant ENSG00000226622:n.288+11734A>G (chr2-62578767-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000664749.1(ENSG00000226622):n.288+11734A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,066 control chromosomes in the GnomAD database, including 34,490 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 0.67 ( 34490 hom., cov: 32)

Consequence

ENSG00000226622
ENST00000664749.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.45

Publications

5 publications found

Variant links:

Genes affected

ENSG00000226622 (HGNC:):

ENSG00000226622 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000226622	ENST00000664749.1 link	n.288+11734A>G	intron_variant	Intron 3 of 3
ENSG00000226622	ENST00000668814.1 link	n.305-123A>G	intron_variant	Intron 4 of 4
ENSG00000228541	ENST00000807713.1 link	n.400+14902T>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.671

AC:

101965

AN:

151948

Hom.:

34460

Cov.:

show subpopulations

Gnomad AFR

AF:

0.741

Gnomad AMI

AF:

0.714

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.567

Gnomad EAS

AF:

0.729

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.643

Gnomad OTH

AF:

0.651

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

GnomAD4 genome

AF:

0.671

AC:

102053

AN:

152066

Hom.:

34490

Cov.:

AF XY:

0.669

AC XY:

49695

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.741

AC:

30713

AN:

41474

American (AMR)

AF:

0.643

AC:

9823

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.567

AC:

1966

AN:

3466

East Asian (EAS)

AF:

0.730

AC:

3776

AN:

5174

South Asian (SAS)

AF:

0.648

AC:

3122

AN:

4818

European-Finnish (FIN)

AF:

0.643

AC:

6794

AN:

10562

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.643

AC:

43682

AN:

67970

Other (OTH)

AF:

0.655

AC:

1383

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1702

3405

5107

6810

8512

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.648

Hom.:

13879

Bravo

AF:

0.677

Asia WGS

AF:

0.736

AC:

2560

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

1.4

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