dbSNP rs2703862: ENSG00000253363:n.530-591G>T (chr8-36538067-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000524132.6(ENSG00000253363):n.530-591G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,902 control chromosomes in the GnomAD database, including 1,431 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 0.13 ( 1431 hom., cov: 31)

Consequence

ENSG00000253363
ENST00000524132.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

5 publications found

Variant links:

Genes affected

ENSG00000253363 (HGNC:):

ENSG00000253363 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000253363	ENST00000524132.6 link	n.530-591G>T	intron_variant	Intron 4 of 4	4
ENSG00000253363	ENST00000651399.1 link	n.517-42355G>T	intron_variant	Intron 4 of 5
ENSG00000253363	ENST00000656455.2 link	n.485-111003G>T	intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19577

AN:

151786

Hom.:

1433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.150

Gnomad NFE

AF:

0.0965

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.129

AC:

19584

AN:

151902

Hom.:

1431

Cov.:

AF XY:

0.132

AC XY:

9785

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.171

AC:

7075

AN:

41424

American (AMR)

AF:

0.112

AC:

1703

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

424

AN:

3468

East Asian (EAS)

AF:

0.283

AC:

1454

AN:

5136

South Asian (SAS)

AF:

0.200

AC:

963

AN:

4816

European-Finnish (FIN)

AF:

0.101

AC:

1066

AN:

10526

Middle Eastern (MID)

AF:

0.158

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0965

AC:

6555

AN:

67956

Other (OTH)

AF:

0.136

AC:

288

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

864

1728

2593

3457

4321

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.109

Hom.:

574

Bravo

AF:

0.129

Asia WGS

AF:

0.251

AC:

868

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.94

(source)

DANN

Benign

0.77

PhyloP100

-1.4

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