Genetic Variant ENST00000827042.1:n.446+1523C>A (chr5-173507895-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 ENST00000827042.1(ENSG00000253968):n.446+1523C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,954 control chromosomes in the GnomAD database, including 12,003 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 0.40 ( 12003 hom., cov: 31)

Consequence

ENSG00000253968
ENST00000827042.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00900

Publications

9 publications found

Variant links:

COSMIC-nc: COSV60232117

Genes affected

ENSG00000253968 (HGNC:):

ENSG00000253968 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1 link	n.3056+305C>A		intron_variant	Intron 14 of 14
LOC105377732	XR_007059057.1 link	n.4116+305C>A		intron_variant	Intron 17 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253968	ENST00000827042.1 link	n.446+1523C>A		intron_variant	Intron 2 of 2
ENSG00000253968	ENST00000827044.1 link	n.374+1523C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

60003

AN:

151836

Hom.:

11970

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.480

Gnomad ASJ

AF:

0.339

Gnomad EAS

AF:

0.294

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.388

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.416

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

GnomAD4 genome

AF:

0.395

AC:

60091

AN:

151954

Hom.:

12003

Cov.:

AF XY:

0.399

AC XY:

29606

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.387

AC:

16018

AN:

41436

American (AMR)

AF:

0.480

AC:

7338

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

1178

AN:

3472

East Asian (EAS)

AF:

0.294

AC:

1520

AN:

5164

South Asian (SAS)

AF:

0.419

AC:

2015

AN:

4810

European-Finnish (FIN)

AF:

0.388

AC:

4101

AN:

10564

Middle Eastern (MID)

AF:

0.340

AC:

100

AN:

294

European-Non Finnish (NFE)

AF:

0.391

AC:

26538

AN:

67916

Other (OTH)

AF:

0.421

AC:

888

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1827

3655

5482

7310

9137

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.365

Hom.:

3936

Bravo

AF:

0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.47

(source)

DANN

Benign

0.84

PhyloP100

-0.0090

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

ENST00000827042.1:n.446+1523C>A

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