Genetic Variant ENSG00000302600:n.85-2336A>G (chr9-69783599-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000788064.1(ENSG00000302600):n.85-2336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,966 control chromosomes in the GnomAD database, including 939 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 0.10 ( 939 hom., cov: 32)

Consequence

ENSG00000302600
ENST00000788064.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215

Publications

2 publications found

Variant links:

Genes affected

ENSG00000302600 (HGNC:):

ENSG00000302600 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376076	XR_929908.2 link	n.380-2336A>G	intron_variant	Intron 1 of 3
LOC105376076	XR_929909.3 link	n.75-2336A>G	intron_variant	Intron 1 of 3
LOC105376076	XR_929910.3 link	n.380-2336A>G	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302600	ENST00000788064.1 link	n.85-2336A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15635

AN:

151848

Hom.:

941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0907

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0938

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.103

AC:

15635

AN:

151966

Hom.:

939

Cov.:

AF XY:

0.107

AC XY:

7925

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.0907

AC:

3761

AN:

41478

American (AMR)

AF:

0.106

AC:

1624

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

411

AN:

3470

East Asian (EAS)

AF:

0.264

AC:

1362

AN:

5166

South Asian (SAS)

AF:

0.148

AC:

712

AN:

4814

European-Finnish (FIN)

AF:

0.102

AC:

1073

AN:

10492

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0938

AC:

6372

AN:

67954

Other (OTH)

AF:

0.106

AC:

223

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

705

1410

2114

2819

3524

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.0984

Hom.:

1441

Bravo

AF:

0.104

Asia WGS

AF:

0.168

AC:

586

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.9

(source)

DANN

Benign

0.58

PhyloP100

0.21

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