Genetic Variant ENSG00000299951:n.241-3797A>G (chr1-187692398-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000767639.1(ENSG00000299951):n.241-3797A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,874 control chromosomes in the GnomAD database, including 11,326 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 0.36 ( 11326 hom., cov: 31)

Consequence

ENSG00000299951
ENST00000767639.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242

Publications

2 publications found

Variant links:

Genes affected

ENSG00000299951 (HGNC:):

ENSG00000299951 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 (NFE) allele frequency at 95% confidence interval = 0.472 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
ENSG00000299951	ENST00000767639.1 link	n.241-3797A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

54254

AN:

151756

Hom.:

11331

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.0150

Gnomad SAS

AF:

0.275

Gnomad FIN

AF:

0.490

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.394

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

GnomAD4 genome

AF:

0.357

AC:

54252

AN:

151874

Hom.:

11326

Cov.:

AF XY:

0.353

AC XY:

26183

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.178

AC:

7374

AN:

41430

American (AMR)

AF:

0.335

AC:

5099

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.438

AC:

1519

AN:

3468

East Asian (EAS)

AF:

0.0151

AC:

AN:

5174

South Asian (SAS)

AF:

0.276

AC:

1330

AN:

4818

European-Finnish (FIN)

AF:

0.490

AC:

5169

AN:

10552

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.477

AC:

32353

AN:

67896

Other (OTH)

AF:

0.390

AC:

823

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1617

3235

4852

6470

8087

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.443

Hom.:

25961

Bravo

AF:

0.338

Asia WGS

AF:

0.146

AC:

513

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

4.2

(source)

DANN

Benign

0.69

PhyloP100

-0.24

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