Genetic Variant ENSG00000286980:n.550-22349C>T (chr2-184357809-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000671393.1(ENSG00000286980):n.550-22349C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00933 in 143,862 control chromosomes in the GnomAD database, including 25 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 0.0093 ( 25 hom., cov: 31)

Consequence

ENSG00000286980
ENST00000671393.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145

Publications

0 publications found

Variant links:

Genes affected

ENSG00000286980 (HGNC:):

ENSG00000286980 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105373776	XR_001739817.2 link	n.121+2526G>A	intron_variant	Intron 2 of 4
LOC102724340	XR_001739819.1 link	n.318+24916C>T	intron_variant	Intron 3 of 4
LOC105373776	XR_923647.3 link	n.191+2526G>A	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286980	ENST00000671393.1 link	n.550-22349C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.00933

AC:

1342

AN:

143810

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00559

Gnomad AMI

AF:

0.0455

Gnomad AMR

AF:

0.00232

Gnomad ASJ

AF:

0.00118

Gnomad EAS

AF:

0.0760

Gnomad SAS

AF:

0.0168

Gnomad FIN

AF:

0.0132

Gnomad MID

AF:

0.0201

Gnomad NFE

AF:

0.00715

Gnomad OTH

AF:

0.00755

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

GnomAD4 genome

AF:

0.00933

AC:

1342

AN:

143862

Hom.:

Cov.:

AF XY:

0.00990

AC XY:

689

AN XY:

69630

show subpopulations

African (AFR)

AF:

0.00568

AC:

223

AN:

39288

American (AMR)

AF:

0.00232

AC:

AN:

14234

Ashkenazi Jewish (ASJ)

AF:

0.00118

AC:

AN:

3388

East Asian (EAS)

AF:

0.0755

AC:

362

AN:

4792

South Asian (SAS)

AF:

0.0166

AC:

AN:

4334

European-Finnish (FIN)

AF:

0.0132

AC:

114

AN:

8652

Middle Eastern (MID)

AF:

0.0182

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.00715

AC:

472

AN:

66000

Other (OTH)

AF:

0.00801

AC:

AN:

1998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

124

187

249

311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00643

Hom.:

Bravo

AF:

0.00869

Asia WGS

AF:

0.0300

AC:

104

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.9

(source)

DANN

Benign

0.62

PhyloP100

-0.14

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