Genetic Variant ENSG00000299216:n.241+1369T>G (chr16-13806476-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000761632.1(ENSG00000299216):n.241+1369T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,152 control chromosomes in the GnomAD database, including 6,772 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 0.28 ( 6772 hom., cov: 33)

Consequence

ENSG00000299216
ENST00000761632.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.592

Publications

3 publications found

Variant links:

Genes affected

ENSG00000299216 (HGNC:):

ENSG00000299216 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903646	XR_007064997.1 link	n.234+1369T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299216	ENST00000761632.1 link	n.241+1369T>G		intron_variant	Intron 1 of 1
ENSG00000299216	ENST00000761633.1 link	n.119+1485T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42465

AN:

152034

Hom.:

6761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.198

Gnomad OTH

AF:

0.278

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

GnomAD4 genome

AF:

0.279

AC:

42520

AN:

152152

Hom.:

6772

Cov.:

AF XY:

0.283

AC XY:

21088

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.398

AC:

16489

AN:

41460

American (AMR)

AF:

0.292

AC:

4457

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.351

AC:

1215

AN:

3466

East Asian (EAS)

AF:

0.472

AC:

2444

AN:

5180

South Asian (SAS)

AF:

0.348

AC:

1681

AN:

4826

European-Finnish (FIN)

AF:

0.182

AC:

1934

AN:

10604

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.198

AC:

13495

AN:

68010

Other (OTH)

AF:

0.279

AC:

590

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1514

3028

4542

6056

7570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<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:

0.243

Hom.:

7000

Bravo

AF:

0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.14

(source)

DANN

Benign

0.73

PhyloP100

-0.59

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