Genetic Variant ENSG00000288692:n.616+93361T>C (chr4-111210633-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000681682.2(ENSG00000288692):n.616+93361T>C variant causes a intron change. The variant allele was found at a frequency of 0.49 in 151,966 control chromosomes in the GnomAD database, including 19,347 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 0.49 ( 19347 hom., cov: 33)

Consequence

ENSG00000288692
ENST00000681682.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.62

Publications

5 publications found

Variant links:

Genes affected

ENSG00000288692 (HGNC:):

ENSG00000288692 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288692	ENST00000681682.2 link	n.616+93361T>C	intron_variant	Intron 3 of 5
ENSG00000300136	ENST00000769402.1 link	n.275+4206A>G	intron_variant	Intron 2 of 2
ENSG00000300136	ENST00000769403.1 link	n.276-1311A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74512

AN:

151848

Hom.:

19341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.610

Gnomad MID

AF:

0.433

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.473

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

GnomAD4 genome

AF:

0.490

AC:

74536

AN:

151966

Hom.:

19347

Cov.:

AF XY:

0.495

AC XY:

36778

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.318

AC:

13171

AN:

41480

American (AMR)

AF:

0.491

AC:

7479

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

1664

AN:

3472

East Asian (EAS)

AF:

0.481

AC:

2476

AN:

5144

South Asian (SAS)

AF:

0.591

AC:

2846

AN:

4816

European-Finnish (FIN)

AF:

0.610

AC:

6447

AN:

10566

Middle Eastern (MID)

AF:

0.408

AC:

119

AN:

292

European-Non Finnish (NFE)

AF:

0.574

AC:

38972

AN:

67932

Other (OTH)

AF:

0.473

AC:

999

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1900

3800

5701

7601

9501

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

670

1340

2010

2680

3350

<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:

0.542

Hom.:

96562

Bravo

AF:

0.470

Asia WGS

AF:

0.510

AC:

1773

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Benign

0.74

PhyloP100

3.6

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