Genetic Variant ENSG00000243797:n.172+1130C>T (chr7-106759436-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 ENST00000592441.1(ENSG00000243797):n.172+1130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,060 control chromosomes in the GnomAD database, including 1,123 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 0.11 ( 1123 hom., cov: 32)

Consequence

ENSG00000243797
ENST00000592441.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.813

Publications

5 publications found

Variant links:

Genes affected

ENSG00000243797 (HGNC:):

ENSG00000243797 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 (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243797	ENST00000592441.1 link	n.172+1130C>T		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17392

AN:

151942

Hom.:

1127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0671

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.111

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

GnomAD4 genome

AF:

0.114

AC:

17397

AN:

152060

Hom.:

1123

Cov.:

AF XY:

0.114

AC XY:

8500

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.0671

AC:

2785

AN:

41496

American (AMR)

AF:

0.124

AC:

1900

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

402

AN:

3470

East Asian (EAS)

AF:

0.103

AC:

534

AN:

5172

South Asian (SAS)

AF:

0.209

AC:

1007

AN:

4824

European-Finnish (FIN)

AF:

0.135

AC:

1422

AN:

10542

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.132

AC:

8953

AN:

67980

Other (OTH)

AF:

0.109

AC:

231

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

788

1576

2364

3152

3940

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.124

Hom.:

2080

Bravo

AF:

0.109

Asia WGS

AF:

0.152

AC:

526

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.8

(source)

DANN

Benign

0.68

PhyloP100

0.81

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