dbSNP rs16919696: ENSG00000254394:n.254-56328G>A (chr8-82847327-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000658531.1(ENSG00000254394):n.254-56328G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 86,686 control chromosomes in the GnomAD database, including 257 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 0.055 ( 257 hom., cov: 30)

Consequence

ENSG00000254394
ENST00000658531.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.318

Publications

0 publications found

Variant links:

Genes affected

ENSG00000254394 (HGNC:):

ENSG00000254394 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 = 0.167 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
ENSG00000254394	ENST00000658531.1 link	n.254-56328G>A		intron_variant	Intron 3 of 3
ENSG00000254394	ENST00000663058.1 link	n.944-65612G>A		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.0554

AC:

4795

AN:

86624

Hom.:

258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0339

Gnomad ASJ

AF:

0.000831

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00168

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00450

Gnomad NFE

AF:

0.00101

Gnomad OTH

AF:

0.0492

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

GnomAD4 genome

AF:

0.0553

AC:

4794

AN:

86686

Hom.:

257

Cov.:

AF XY:

0.0539

AC XY:

2277

AN XY:

42252

show subpopulations

African (AFR)

AF:

0.171

AC:

4432

AN:

25852

American (AMR)

AF:

0.0338

AC:

258

AN:

7622

Ashkenazi Jewish (ASJ)

AF:

0.000831

AC:

AN:

2408

East Asian (EAS)

AF:

0.00

AC:

AN:

2238

South Asian (SAS)

AF:

0.00126

AC:

AN:

2388

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5626

Middle Eastern (MID)

AF:

0.00485

AC:

AN:

206

European-Non Finnish (NFE)

AF:

0.00101

AC:

AN:

38662

Other (OTH)

AF:

0.0491

AC:

AN:

1202

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

197

394

592

789

986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.00475

Hom.:

Bravo

AF:

0.0373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.4

(source)

DANN

Benign

0.58

PhyloP100

-0.32

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