Genetic Variant ENST00000521294.1:n.121-16518T>C (chr8-51304202-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 ENST00000521294.1(ENSG00000253664):n.121-16518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,976 control chromosomes in the GnomAD database, including 9,721 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 0.33 ( 9721 hom., cov: 31)

Consequence

ENSG00000253664
ENST00000521294.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

8 publications found

Variant links:

Genes affected

ENSG00000253664 (HGNC:):

ENSG00000253664 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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
ENSG00000253664	ENST00000521294.1 link	n.121-16518T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.329

AC:

50035

AN:

151858

Hom.:

9685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.542

Gnomad AMI

AF:

0.178

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.320

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

GnomAD4 genome

AF:

0.330

AC:

50124

AN:

151976

Hom.:

9721

Cov.:

AF XY:

0.322

AC XY:

23947

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.543

AC:

22492

AN:

41416

American (AMR)

AF:

0.250

AC:

3810

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

969

AN:

3466

East Asian (EAS)

AF:

0.141

AC:

731

AN:

5168

South Asian (SAS)

AF:

0.218

AC:

1049

AN:

4820

European-Finnish (FIN)

AF:

0.222

AC:

2338

AN:

10544

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17799

AN:

67974

Other (OTH)

AF:

0.320

AC:

676

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1570

3140

4711

6281

7851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.288

Hom.:

12850

Bravo

AF:

0.340

Asia WGS

AF:

0.238

AC:

829

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.26

(source)

DANN

Benign

0.69

PhyloP100

-1.1

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