Genetic Variant ENSG00000288016:n.196+24095C>T (chr13-84111092-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000653443.1(ENSG00000288016):n.196+24095C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,074 control chromosomes in the GnomAD database, including 3,348 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 0.18 ( 3348 hom., cov: 32)

Consequence

ENSG00000288016
ENST00000653443.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.198

Publications

0 publications found

Variant links:

Genes affected

ENSG00000288016 (HGNC:):

ENSG00000288016 links:

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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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288016	ENST00000653443.1 link	n.196+24095C>T	intron_variant	Intron 1 of 4
ENSG00000288016	ENST00000691679.2 link	n.262-20328C>T	intron_variant	Intron 1 of 1
ENSG00000288016	ENST00000701394.1 link	n.253-9380C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27536

AN:

151956

Hom.:

3328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.0938

Gnomad FIN

AF:

0.0874

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.180

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

GnomAD4 genome

AF:

0.182

AC:

27611

AN:

152074

Hom.:

3348

Cov.:

AF XY:

0.181

AC XY:

13452

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.341

AC:

14154

AN:

41470

American (AMR)

AF:

0.199

AC:

3039

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

489

AN:

3472

East Asian (EAS)

AF:

0.212

AC:

1092

AN:

5150

South Asian (SAS)

AF:

0.0947

AC:

456

AN:

4814

European-Finnish (FIN)

AF:

0.0874

AC:

926

AN:

10596

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.103

AC:

6988

AN:

67974

Other (OTH)

AF:

0.180

AC:

380

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1060

2121

3181

4242

5302

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.161

Hom.:

408

Bravo

AF:

0.198

Asia WGS

AF:

0.155

AC:

536

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.5

(source)

DANN

Benign

0.39

PhyloP100

0.20

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