Genetic Variant ENSG00000242593:n.295-6340T>C (chr7-124369982-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000484322.5(ENSG00000242593):n.295-6340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,824 control chromosomes in the GnomAD database, including 4,445 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 0.23 ( 4445 hom., cov: 32)

Consequence

ENSG00000242593
ENST00000484322.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.692

Publications

2 publications found

Variant links:

Genes affected

ENSG00000242593 (HGNC:):

ENSG00000242593 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 (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000242593	ENST00000484322.5 link	n.295-6340T>C	intron_variant	Intron 4 of 8	1
ENSG00000241324	ENST00000470677.2 link	n.220-20058A>G	intron_variant	Intron 2 of 4	2
ENSG00000242593	ENST00000650961.1 link	n.1247-6340T>C	intron_variant	Intron 6 of 10

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34263

AN:

151706

Hom.:

4443

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.402

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.251

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

GnomAD4 genome

AF:

0.226

AC:

34265

AN:

151824

Hom.:

4445

Cov.:

AF XY:

0.220

AC XY:

16307

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.131

AC:

5422

AN:

41488

American (AMR)

AF:

0.205

AC:

3125

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

1123

AN:

3470

East Asian (EAS)

AF:

0.140

AC:

725

AN:

5166

South Asian (SAS)

AF:

0.122

AC:

589

AN:

4818

European-Finnish (FIN)

AF:

0.231

AC:

2416

AN:

10444

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.293

AC:

19875

AN:

67898

Other (OTH)

AF:

0.249

AC:

525

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1268

2536

3805

5073

6341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.275

Hom.:

10474

Bravo

AF:

0.220

Asia WGS

AF:

0.155

AC:

535

AN:

3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.1

(source)

DANN

Benign

0.69

PhyloP100

0.69

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