Genetic Variant ENSG00000297854:n.110+11957G>A (chr5-36541200-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 ENST00000751409.1(ENSG00000297854):n.110+11957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,010 control chromosomes in the GnomAD database, including 14,395 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 0.40 ( 14395 hom., cov: 33)

Consequence

ENSG00000297854
ENST00000751409.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.222

Publications

2 publications found

Variant links:

Genes affected

ENSG00000297854 (HGNC:):

ENSG00000297854 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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
ENSG00000297854	ENST00000751409.1 link	n.110+11957G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.398

AC:

60498

AN:

151892

Hom.:

14349

Cov.:

show subpopulations

Gnomad AFR

AF:

0.669

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.402

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.361

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

GnomAD4 genome

AF:

0.399

AC:

60604

AN:

152010

Hom.:

14395

Cov.:

AF XY:

0.398

AC XY:

29569

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.670

AC:

27772

AN:

41470

American (AMR)

AF:

0.286

AC:

4373

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.239

AC:

830

AN:

3472

East Asian (EAS)

AF:

0.133

AC:

687

AN:

5178

South Asian (SAS)

AF:

0.197

AC:

947

AN:

4814

European-Finnish (FIN)

AF:

0.402

AC:

4235

AN:

10528

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20799

AN:

67958

Other (OTH)

AF:

0.360

AC:

762

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1662

3324

4985

6647

8309

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<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:

0.315

Hom.:

13947

Bravo

AF:

0.401

Asia WGS

AF:

0.214

AC:

746

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

0.99

(source)

DANN

Benign

0.54

PhyloP100

-0.22

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