Genetic Variant ENSG00000305582:n.65+1778A>C (chr2-218154394-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000811769.1(ENSG00000305582):n.65+1778A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 128,288 control chromosomes in the GnomAD database, including 121 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 0.030 ( 121 hom., cov: 26)

Consequence

ENSG00000305582
ENST00000811769.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.144

Publications

4 publications found

Variant links:

Genes affected

ENSG00000305582 (HGNC:):

ENSG00000305582 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0809 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
ENSG00000305582	ENST00000811769.1 link	n.65+1778A>C		intron_variant	Intron 1 of 2
ENSG00000305582	ENST00000811770.1 link	n.66-261A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0296

AC:

3793

AN:

128244

Hom.:

121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0834

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0137

Gnomad ASJ

AF:

0.00252

Gnomad EAS

AF:

0.00350

Gnomad SAS

AF:

0.00285

Gnomad FIN

AF:

0.0113

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00902

Gnomad OTH

AF:

0.0245

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

GnomAD4 genome

AF:

0.0296

AC:

3799

AN:

128288

Hom.:

121

Cov.:

AF XY:

0.0292

AC XY:

1796

AN XY:

61524

show subpopulations

African (AFR)

AF:

0.0834

AC:

2935

AN:

35202

American (AMR)

AF:

0.0137

AC:

173

AN:

12614

Ashkenazi Jewish (ASJ)

AF:

0.00252

AC:

AN:

3178

East Asian (EAS)

AF:

0.00351

AC:

AN:

4272

South Asian (SAS)

AF:

0.00261

AC:

AN:

3838

European-Finnish (FIN)

AF:

0.0113

AC:

AN:

6890

Middle Eastern (MID)

AF:

0.00388

AC:

AN:

258

European-Non Finnish (NFE)

AF:

0.00903

AC:

537

AN:

59500

Other (OTH)

AF:

0.0244

AC:

AN:

1724

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

137

274

411

548

685

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<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:

0.0166

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.6

(source)

DANN

Benign

0.56

PhyloP100

0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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