Genetic Variant ENSG00000293607:n.263-37743T>G (chr9-73149649-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715863.1(ENSG00000293607):n.263-37743T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,140 control chromosomes in the GnomAD database, including 509 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 0.074 ( 509 hom., cov: 32)

Consequence

ENSG00000293607
ENST00000715863.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.42

Publications

16 publications found

Variant links:

Genes affected

ENSG00000293607 (HGNC:):

ENSG00000293607 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=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000293607	ENST00000715863.1 link	n.263-37743T>G	intron_variant	Intron 2 of 3
ENSG00000293607	ENST00000719114.1 link	n.207-37743T>G	intron_variant	Intron 1 of 2
ENSG00000293607	ENST00000719115.1 link	n.134-37743T>G	intron_variant	Intron 2 of 3
ENSG00000293607	ENST00000719116.1 link	n.139-37743T>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0737

AC:

11201

AN:

152022

Hom.:

509

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.0548

Gnomad ASJ

AF:

0.0786

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.0513

Gnomad FIN

AF:

0.0322

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0413

Gnomad OTH

AF:

0.0684

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

GnomAD4 genome

AF:

0.0736

AC:

11204

AN:

152140

Hom.:

509

Cov.:

AF XY:

0.0727

AC XY:

5405

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.137

AC:

5668

AN:

41508

American (AMR)

AF:

0.0548

AC:

837

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0786

AC:

273

AN:

3472

East Asian (EAS)

AF:

0.163

AC:

843

AN:

5170

South Asian (SAS)

AF:

0.0509

AC:

245

AN:

4810

European-Finnish (FIN)

AF:

0.0322

AC:

341

AN:

10606

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0413

AC:

2809

AN:

67972

Other (OTH)

AF:

0.0668

AC:

141

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

543

1086

1629

2172

2715

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0562

Hom.:

1247

Bravo

AF:

0.0816

Asia WGS

AF:

0.104

AC:

363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

5.7

(source)

DANN

Benign

0.75

PhyloP100

-1.4

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