Genetic Variant ENST00000804953.1:n.130+5779T>C (chr8-5516018-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 ENST00000804953.1(ENSG00000304614):n.130+5779T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,018 control chromosomes in the GnomAD database, including 3,222 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 0.20 ( 3222 hom., cov: 32)

Consequence

ENSG00000304614
ENST00000804953.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

Publications

0 publications found

Variant links:

Genes affected

ENSG00000304614 (HGNC:):

ENSG00000304614 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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
ENSG00000304614	ENST00000804953.1 link	n.130+5779T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30726

AN:

151898

Hom.:

3222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.324

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.223

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

GnomAD4 genome

AF:

0.202

AC:

30735

AN:

152018

Hom.:

3222

Cov.:

AF XY:

0.199

AC XY:

14772

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.154

AC:

6395

AN:

41496

American (AMR)

AF:

0.200

AC:

3055

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

858

AN:

3468

East Asian (EAS)

AF:

0.259

AC:

1327

AN:

5124

South Asian (SAS)

AF:

0.236

AC:

1134

AN:

4810

European-Finnish (FIN)

AF:

0.129

AC:

1365

AN:

10602

Middle Eastern (MID)

AF:

0.295

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.232

AC:

15752

AN:

67930

Other (OTH)

AF:

0.221

AC:

468

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1250

2500

3750

5000

6250

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.222

Hom.:

7105

Bravo

AF:

0.206

Asia WGS

AF:

0.234

AC:

812

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

0.12

(source)

DANN

Benign

0.20

PhyloP100

-1.9

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