Genetic Variant ENSG00000293066:n.210+15752C>A (chr6-39964255-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000649703.2(ENSG00000293066):n.210+15752C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,106 control chromosomes in the GnomAD database, including 10,925 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 ( 10925 hom., cov: 33)

Consequence

ENSG00000293066
ENST00000649703.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

3 publications found

Variant links:

Genes affected

ENSG00000293066 (HGNC:):

ENSG00000293066 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723789	XR_001744112.1 link	n.259+696C>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000293066	ENST00000649703.2 link	n.210+15752C>A	intron_variant	Intron 3 of 4
ENSG00000293066	ENST00000741538.1 link	n.256+15752C>A	intron_variant	Intron 3 of 5
ENSG00000293066	ENST00000741539.1 link	n.153+696C>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

54414

AN:

151988

Hom.:

10919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.462

Gnomad EAS

AF:

0.383

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.456

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.380

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

GnomAD4 genome

AF:

0.358

AC:

54423

AN:

152106

Hom.:

10925

Cov.:

AF XY:

0.364

AC XY:

27083

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.161

AC:

6676

AN:

41514

American (AMR)

AF:

0.491

AC:

7505

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.462

AC:

1604

AN:

3470

East Asian (EAS)

AF:

0.384

AC:

1982

AN:

5168

South Asian (SAS)

AF:

0.511

AC:

2461

AN:

4820

European-Finnish (FIN)

AF:

0.456

AC:

4822

AN:

10574

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.410

AC:

27843

AN:

67958

Other (OTH)

AF:

0.380

AC:

803

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1706

3412

5117

6823

8529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

530

1060

1590

2120

2650

<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:

0.309

Hom.:

1311

Bravo

AF:

0.350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.71

(source)

DANN

Benign

0.74

PhyloP100

-1.0

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