Genetic Variant ENST00000807627.1:n.223-33710C>A (chr2-175524333-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000807627.1(ENSG00000305006):n.223-33710C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 152,188 control chromosomes in the GnomAD database, including 820 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 0.090 ( 820 hom., cov: 32)

Consequence

ENSG00000305006
ENST00000807627.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104

Publications

6 publications found

Variant links:

Genes affected

ENSG00000305006 (HGNC:):

ENSG00000305006 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.137 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
ENSG00000305006	ENST00000807627.1 link	n.223-33710C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0903

AC:

13738

AN:

152070

Hom.:

821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0259

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.0667

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.102

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

GnomAD4 genome

AF:

0.0903

AC:

13739

AN:

152188

Hom.:

820

Cov.:

AF XY:

0.0888

AC XY:

6604

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0259

AC:

1075

AN:

41544

American (AMR)

AF:

0.142

AC:

2169

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

382

AN:

3470

East Asian (EAS)

AF:

0.00154

AC:

AN:

5180

South Asian (SAS)

AF:

0.103

AC:

497

AN:

4818

European-Finnish (FIN)

AF:

0.0667

AC:

707

AN:

10600

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8289

AN:

67980

Other (OTH)

AF:

0.101

AC:

213

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

640

1280

1920

2560

3200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.113

Hom.:

186

Bravo

AF:

0.0938

Asia WGS

AF:

0.0340

AC:

119

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.71

(source)

DANN

Benign

0.73

PhyloP100

-0.10

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