Genetic Variant ENST00000637807.1:c.2373+23844G>A (chr7-17364072-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000637807.1(ENSG00000283321):c.2373+23844G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,064 control chromosomes in the GnomAD database, including 3,034 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 0.17 ( 3034 hom., cov: 32)

Consequence

ENSG00000283321
ENST00000637807.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

1 publications found

Variant links:

Genes affected

ENSG00000283321 (HGNC:):

ENSG00000283321 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375171	XR_927074.3 link	n.212+244C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283321	ENST00000637807.1 link	c.2373+23844G>A		intron_variant	Intron 10 of 11	5		ENSP00000490530.1		A0A1B0GVI7

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26390

AN:

151946

Hom.:

3023

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.147

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

GnomAD4 genome

AF:

0.174

AC:

26440

AN:

152064

Hom.:

3034

Cov.:

AF XY:

0.174

AC XY:

12972

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.307

AC:

12719

AN:

41460

American (AMR)

AF:

0.137

AC:

2097

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

440

AN:

3468

East Asian (EAS)

AF:

0.382

AC:

1977

AN:

5172

South Asian (SAS)

AF:

0.158

AC:

760

AN:

4818

European-Finnish (FIN)

AF:

0.106

AC:

1116

AN:

10566

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6885

AN:

67986

Other (OTH)

AF:

0.145

AC:

307

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1068

2136

3203

4271

5339

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<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:

0.119

Hom.:

1506

Bravo

AF:

0.183

Asia WGS

AF:

0.231

AC:

800

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.034

(source)

DANN

Benign

0.45

PhyloP100

-1.3

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