Genetic Variant ENSG00000248656:n.171-35789G>A (chr4-111582716-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 ENST00000681880.1(ENSG00000248656):n.171-35789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,188 control chromosomes in the GnomAD database, including 1,149 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 0.10 ( 1149 hom., cov: 32)

Consequence

ENSG00000248656
ENST00000681880.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.168

Publications

6 publications found

Variant links:

Genes affected

ENSG00000248656 (HGNC:):

ENSG00000248656 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 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
ENSG00000248656	ENST00000681880.1 link	n.171-35789G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15878

AN:

152070

Hom.:

1149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0281

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.0797

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.0976

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

GnomAD4 genome

AF:

0.104

AC:

15866

AN:

152188

Hom.:

1149

Cov.:

AF XY:

0.102

AC XY:

7602

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0280

AC:

1164

AN:

41540

American (AMR)

AF:

0.0795

AC:

1213

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

376

AN:

3472

East Asian (EAS)

AF:

0.00174

AC:

AN:

5184

South Asian (SAS)

AF:

0.133

AC:

642

AN:

4830

European-Finnish (FIN)

AF:

0.136

AC:

1438

AN:

10582

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10676

AN:

67998

Other (OTH)

AF:

0.0961

AC:

203

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

693

1386

2078

2771

3464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.141

Hom.:

1914

Bravo

AF:

0.0949

Asia WGS

AF:

0.0560

AC:

195

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.0

(source)

DANN

Benign

0.52

PhyloP100

-0.17

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