dbSNP rs6050164: ENSG00000301203:n.75+15782T>C (chr20-24934659-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000776975.1(ENSG00000301203):n.75+15782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 152,302 control chromosomes in the GnomAD database, including 698 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 ( 698 hom., cov: 33)

Consequence

ENSG00000301203
ENST00000776975.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Publications

2 publications found

Variant links:

Genes affected

ENSG00000301203 (HGNC:):

ENSG00000301203 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 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
ENSG00000301203	ENST00000776975.1 link	n.75+15782T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0899

AC:

13676

AN:

152182

Hom.:

698

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0993

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0788

Gnomad ASJ

AF:

0.0614

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0971

Gnomad FIN

AF:

0.0417

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0918

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

GnomAD4 genome

AF:

0.0899

AC:

13693

AN:

152302

Hom.:

698

Cov.:

AF XY:

0.0864

AC XY:

6434

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.0995

AC:

4133

AN:

41556

American (AMR)

AF:

0.0786

AC:

1203

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.0614

AC:

213

AN:

3470

East Asian (EAS)

AF:

0.00212

AC:

AN:

5184

South Asian (SAS)

AF:

0.0967

AC:

467

AN:

4828

European-Finnish (FIN)

AF:

0.0417

AC:

443

AN:

10630

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6923

AN:

68002

Other (OTH)

AF:

0.0918

AC:

194

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

657

1314

1970

2627

3284

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.0893

Hom.:

117

Bravo

AF:

0.0920

Asia WGS

AF:

0.0590

AC:

206

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.92

(source)

DANN

Benign

0.63

PhyloP100

-1.5

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