Genetic Variant ENSG00000254874:n.146+9656C>T (chr11-92940662-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 ENST00000532770.2(ENSG00000254874):n.146+9656C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,984 control chromosomes in the GnomAD database, including 7,801 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 0.32 ( 7801 hom., cov: 32)

Consequence

ENSG00000254874
ENST00000532770.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0440

Publications

232 publications found

Variant links:

Genes affected

ENSG00000254874 (HGNC:):

ENSG00000254874 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 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
ENSG00000254874	ENST00000532770.2 link	n.146+9656C>T	intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1 link	n.128+9656C>T	intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1 link	n.115+9656C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48157

AN:

151864

Hom.:

7801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.357

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.300

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

GnomAD4 genome

AF:

0.317

AC:

48184

AN:

151984

Hom.:

7801

Cov.:

AF XY:

0.319

AC XY:

23711

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.356

AC:

14774

AN:

41458

American (AMR)

AF:

0.235

AC:

3589

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.278

AC:

961

AN:

3462

East Asian (EAS)

AF:

0.444

AC:

2289

AN:

5154

South Asian (SAS)

AF:

0.390

AC:

1875

AN:

4804

European-Finnish (FIN)

AF:

0.354

AC:

3738

AN:

10548

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.291

AC:

19781

AN:

67962

Other (OTH)

AF:

0.301

AC:

635

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1687

3374

5060

6747

8434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.295

Hom.:

32121

Bravo

AF:

0.308

Asia WGS

AF:

0.354

AC:

1229

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

4.4

(source)

DANN

Benign

0.54

PhyloP100

0.044

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