Genetic Variant ENSG00000224077:n.165-11G>C (chr11-117103213-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000442124.1(ENSG00000224077):n.165-11G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,816 control chromosomes in the GnomAD database, including 15,108 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 0.41 ( 15107 hom., cov: 31)

Exomes 𝑓: 0.35 ( 1 hom. )

Consequence

ENSG00000224077
ENST00000442124.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0320

Publications

28 publications found

Variant links:

Genes affected

ENSG00000224077 (HGNC:):

ENSG00000224077 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000224077	ENST00000442124.1 link	n.165-11G>C	intron_variant	Intron 1 of 2	5
ENSG00000224077	ENST00000750474.1 link	n.541-11G>C	intron_variant	Intron 1 of 2
ENSG00000224077	ENST00000750475.1 link	n.538-11G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62583

AN:

151672

Hom.:

15070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.679

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.282

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.294

Gnomad OTH

AF:

0.359

GnomAD4 exome

AF:

0.346

AC:

AN:

Hom.:

Cov.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.250

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

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.413

AC:

62667

AN:

151790

Hom.:

15107

Cov.:

AF XY:

0.414

AC XY:

30673

AN XY:

74152

show subpopulations

African (AFR)

AF:

0.679

AC:

28115

AN:

41376

American (AMR)

AF:

0.337

AC:

5126

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

1076

AN:

3466

East Asian (EAS)

AF:

0.282

AC:

1458

AN:

5164

South Asian (SAS)

AF:

0.421

AC:

2029

AN:

4818

European-Finnish (FIN)

AF:

0.370

AC:

3882

AN:

10498

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.294

AC:

19950

AN:

67938

Other (OTH)

AF:

0.358

AC:

751

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1666

3332

4999

6665

8331

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<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:

0.193

Hom.:

398

Bravo

AF:

0.423

Asia WGS

AF:

0.395

AC:

1378

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.9

(source)

DANN

Benign

0.40

PhyloP100

0.032

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over