Genetic Variant ENSG00000307577:n.131-28419A>G (chr2-199130145-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 ENST00000827186.1(ENSG00000307577):n.131-28419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,126 control chromosomes in the GnomAD database, including 2,148 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 0.16 ( 2148 hom., cov: 32)

Consequence

ENSG00000307577
ENST00000827186.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.832

Publications

2 publications found

Variant links:

Genes affected

ENSG00000307577 (HGNC:):

ENSG00000307577 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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
ENSG00000307577	ENST00000827186.1 link	n.131-28419A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24748

AN:

152008

Hom.:

2145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.0898

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.163

AC:

24761

AN:

152126

Hom.:

2148

Cov.:

AF XY:

0.159

AC XY:

11848

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.136

AC:

5651

AN:

41488

American (AMR)

AF:

0.213

AC:

3259

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.170

AC:

588

AN:

3464

East Asian (EAS)

AF:

0.315

AC:

1626

AN:

5162

South Asian (SAS)

AF:

0.117

AC:

566

AN:

4822

European-Finnish (FIN)

AF:

0.0898

AC:

951

AN:

10594

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.170

AC:

11577

AN:

68006

Other (OTH)

AF:

0.186

AC:

392

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1064

2128

3191

4255

5319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.162

Hom.:

1114

Bravo

AF:

0.175

Asia WGS

AF:

0.189

AC:

657

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

0.83

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