Genetic Variant ENSG00000286995:n.224-14056G>C (chr7-49570267-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000664348.2(ENSG00000286995):n.224-14056G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,090 control chromosomes in the GnomAD database, including 3,318 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 0.20 ( 3318 hom., cov: 32)

Consequence

ENSG00000286995
ENST00000664348.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286995 (HGNC:):

ENSG00000286995 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901804	XR_007060628.1 link	n.127-14056G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286995	ENST00000664348.2 link	n.224-14056G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30150

AN:

151972

Hom.:

3311

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.186

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

GnomAD4 genome

AF:

0.198

AC:

30185

AN:

152090

Hom.:

3318

Cov.:

AF XY:

0.201

AC XY:

14940

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.130

AC:

5411

AN:

41514

American (AMR)

AF:

0.141

AC:

2158

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

548

AN:

3470

East Asian (EAS)

AF:

0.305

AC:

1576

AN:

5168

South Asian (SAS)

AF:

0.298

AC:

1436

AN:

4824

European-Finnish (FIN)

AF:

0.281

AC:

2964

AN:

10530

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.229

AC:

15545

AN:

67974

Other (OTH)

AF:

0.187

AC:

395

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1199

2398

3598

4797

5996

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.221

Hom.:

479

Bravo

AF:

0.182

Asia WGS

AF:

0.268

AC:

928

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.3

(source)

DANN

Benign

0.29

PhyloP100

0.36

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