Genetic Variant ENSG00000248752:n.472-21569A>G (chr5-125907327-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 ENST00000651847.1(ENSG00000248752):n.472-21569A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,926 control chromosomes in the GnomAD database, including 2,014 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 0.14 ( 2014 hom., cov: 32)

Consequence

ENSG00000248752
ENST00000651847.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.406

Publications

2 publications found

Variant links:

Genes affected

ENSG00000248752 (HGNC:):

ENSG00000248752 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 (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901056	XR_007058919.1 link	n.1775-79321A>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000651847.1 link	n.472-21569A>G		intron_variant	Intron 5 of 15

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21566

AN:

151808

Hom.:

2005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0683

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.418

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.153

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

GnomAD4 genome

AF:

0.142

AC:

21594

AN:

151926

Hom.:

2014

Cov.:

AF XY:

0.145

AC XY:

10777

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.0682

AC:

2832

AN:

41530

American (AMR)

AF:

0.256

AC:

3895

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

482

AN:

3468

East Asian (EAS)

AF:

0.419

AC:

2159

AN:

5152

South Asian (SAS)

AF:

0.222

AC:

1070

AN:

4824

European-Finnish (FIN)

AF:

0.136

AC:

1441

AN:

10614

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.136

AC:

9219

AN:

67816

Other (OTH)

AF:

0.159

AC:

335

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

901

1803

2704

3606

4507

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<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:

0.0139

Hom.:

212

Bravo

AF:

0.150

Asia WGS

AF:

0.329

AC:

1141

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

(source)

DANN

Benign

0.43

PhyloP100

0.41

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