Genetic Variant ENSG00000243797:n.312-15693C>G (chr7-106506823-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000592441.1(ENSG00000243797):n.240-15693C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,136 control chromosomes in the GnomAD database, including 7,919 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 0.31 ( 7919 hom., cov: 32)

Consequence

ENSG00000243797
ENST00000592441.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169

Publications

2 publications found

Variant links:

Genes affected

ENSG00000243797 (HGNC:):

ENSG00000243797 links:

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new If you want to explore the variant's impact on the transcript ENST00000592441.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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 (AMR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000243797	ENST00000485282.5	TSL:3	n.312-15693C>G	intron	N/A
ENSG00000243797	ENST00000490856.5	TSL:4	n.266+13906C>G	intron	N/A
ENSG00000243797	ENST00000592441.1	TSL:2	n.240-15693C>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

46411

AN:

152018

Hom.:

7920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.367

Gnomad OTH

AF:

0.337

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

GnomAD4 genome

AF:

0.305

AC:

46423

AN:

152136

Hom.:

7919

Cov.:

AF XY:

0.305

AC XY:

22716

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.169

AC:

7033

AN:

41514

American (AMR)

AF:

0.430

AC:

6563

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.393

AC:

1363

AN:

3472

East Asian (EAS)

AF:

0.132

AC:

686

AN:

5184

South Asian (SAS)

AF:

0.295

AC:

1423

AN:

4824

European-Finnish (FIN)

AF:

0.300

AC:

3172

AN:

10560

Middle Eastern (MID)

AF:

0.370

AC:

108

AN:

292

European-Non Finnish (NFE)

AF:

0.367

AC:

24969

AN:

67986

Other (OTH)

AF:

0.333

AC:

705

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1610

3220

4829

6439

8049

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

462

924

1386

1848

2310

<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:

0.187

Hom.:

383

Bravo

AF:

0.308

Asia WGS

AF:

0.215

AC:

749

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.4

(source)

DANN

Benign

0.56

PhyloP100

-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over