Genetic Variant ENSG00000292309:n.836-3923G>C (chr7-128220110-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 ENST00000710955.1(ENSG00000292309):n.836-3923G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,004 control chromosomes in the GnomAD database, including 17,920 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 0.48 ( 17920 hom., cov: 32)

Consequence

ENSG00000292309
ENST00000710955.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.338

Publications

33 publications found

Variant links:

Genes affected

ENSG00000292309 (HGNC:):

ENSG00000292309 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901744	XR_007060516.1 link	n.781-3923G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000292309	ENST00000710955.1 link	n.836-3923G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73014

AN:

151886

Hom.:

17913

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.454

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.463

Gnomad EAS

AF:

0.706

Gnomad SAS

AF:

0.444

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.489

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

GnomAD4 genome

AF:

0.481

AC:

73054

AN:

152004

Hom.:

17920

Cov.:

AF XY:

0.482

AC XY:

35838

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.437

AC:

18115

AN:

41442

American (AMR)

AF:

0.436

AC:

6663

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.463

AC:

1605

AN:

3468

East Asian (EAS)

AF:

0.707

AC:

3654

AN:

5170

South Asian (SAS)

AF:

0.444

AC:

2140

AN:

4816

European-Finnish (FIN)

AF:

0.548

AC:

5794

AN:

10580

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.493

AC:

33496

AN:

67948

Other (OTH)

AF:

0.491

AC:

1032

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1928

3857

5785

7714

9642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

654

1308

1962

2616

3270

<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:

0.476

Hom.:

2151

Bravo

AF:

0.469

Asia WGS

AF:

0.581

AC:

2016

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.2

(source)

DANN

Benign

0.40

PhyloP100

0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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