dbSNP rs7267944: ENSG00000300599:n.459-82783T>C (chr20-39318791-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 ENST00000772859.1(ENSG00000300599):n.459-82783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,162 control chromosomes in the GnomAD database, including 5,724 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 0.25 ( 5724 hom., cov: 33)

Consequence

ENSG00000300599
ENST00000772859.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.194

Publications

12 publications found

Variant links:

Genes affected

ENSG00000300599 (HGNC:):

ENSG00000300599 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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
ENSG00000300599	ENST00000772859.1 link	n.459-82783T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38279

AN:

152044

Hom.:

5706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.407

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.239

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

GnomAD4 genome

AF:

0.252

AC:

38336

AN:

152162

Hom.:

5724

Cov.:

AF XY:

0.250

AC XY:

18598

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.407

AC:

16890

AN:

41500

American (AMR)

AF:

0.179

AC:

2732

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

794

AN:

3470

East Asian (EAS)

AF:

0.362

AC:

1873

AN:

5178

South Asian (SAS)

AF:

0.242

AC:

1167

AN:

4826

European-Finnish (FIN)

AF:

0.163

AC:

1728

AN:

10618

Middle Eastern (MID)

AF:

0.250

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.182

AC:

12363

AN:

67970

Other (OTH)

AF:

0.237

AC:

502

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1413

2826

4238

5651

7064

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.205

Hom.:

3741

Bravo

AF:

0.259

Asia WGS

AF:

0.314

AC:

1093

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.3

(source)

DANN

Benign

0.32

PhyloP100

-0.19

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