Genetic Variant ENSG00000224015:n.208-11641T>C (chr5-132149690-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000755558.1(ENSG00000224015):n.208-11641T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,998 control chromosomes in the GnomAD database, including 9,883 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 0.34 ( 9883 hom., cov: 31)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

ENSG00000224015
ENST00000755558.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.261

Publications

22 publications found

Variant links:

COSMIC-nc: COSV70702731

Genes affected

ENSG00000224015 (HGNC:):

ENSG00000224015 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 = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000224015	ENST00000755558.1 link	n.208-11641T>C	intron_variant	Intron 1 of 3
ENSG00000224015	ENST00000755559.1 link	n.281-11641T>C	intron_variant	Intron 1 of 2
ENSG00000224015	ENST00000755560.1 link	n.400-11641T>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51576

AN:

151876

Hom.:

9886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.447

Gnomad OTH

AF:

0.376

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.339

AC:

51571

AN:

151994

Hom.:

9883

Cov.:

AF XY:

0.330

AC XY:

24521

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.183

AC:

7587

AN:

41486

American (AMR)

AF:

0.323

AC:

4934

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

1235

AN:

3470

East Asian (EAS)

AF:

0.209

AC:

1081

AN:

5170

South Asian (SAS)

AF:

0.157

AC:

754

AN:

4808

European-Finnish (FIN)

AF:

0.400

AC:

4218

AN:

10550

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.447

AC:

30353

AN:

67944

Other (OTH)

AF:

0.371

AC:

782

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1641

3282

4924

6565

8206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.362

Hom.:

8962

Bravo

AF:

0.333

Asia WGS

AF:

0.187

AC:

649

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

7.5

(source)

DANN

Benign

0.36

PhyloP100

0.26

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