Genetic Variant ENSG00000261018:n.79C>A (chr9-133633021-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000564021.1(ENSG00000261018):n.79C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,226 control chromosomes in the GnomAD database, including 4,951 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 0.23 ( 4950 hom., cov: 32)

Exomes 𝑓: 0.14 ( 1 hom. )

Consequence

ENSG00000261018
ENST00000564021.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.185

Publications

12 publications found

Variant links:

COSMIC-nc: COSV55040180

Genes affected

ENSG00000261018 (HGNC:):

ENSG00000261018 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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
ENSG00000261018	ENST00000564021.1 link	n.79C>A		non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35711

AN:

152028

Hom.:

4957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.274

Gnomad EAS

AF:

0.666

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.253

GnomAD4 exome

AF:

0.138

AC:

AN:

Hom.:

Cov.:

AF XY:

0.161

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0962

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.581

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:

0.235

AC:

35718

AN:

152146

Hom.:

4950

Cov.:

AF XY:

0.248

AC XY:

18447

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.187

AC:

7768

AN:

41520

American (AMR)

AF:

0.273

AC:

4171

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.274

AC:

950

AN:

3468

East Asian (EAS)

AF:

0.666

AC:

3434

AN:

5158

South Asian (SAS)

AF:

0.461

AC:

2220

AN:

4820

European-Finnish (FIN)

AF:

0.287

AC:

3039

AN:

10584

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.195

AC:

13289

AN:

67992

Other (OTH)

AF:

0.252

AC:

531

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1380

2761

4141

5522

6902

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.205

Hom.:

7710

Bravo

AF:

0.231

Asia WGS

AF:

0.523

AC:

1817

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.74

(source)

DANN

Benign

0.50

PhyloP100

0.18

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