dbSNP rs17693963: ENSG00000302043:n.355+643T>G (chr6-27742386-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 ENST00000783576.1(ENSG00000302043):n.355+643T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 152,234 control chromosomes in the GnomAD database, including 410 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 0.062 ( 410 hom., cov: 32)

Consequence

ENSG00000302043
ENST00000783576.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.202

Publications

67 publications found

Variant links:

Genes affected

ENSG00000302043 (HGNC:):

ENSG00000302043 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000302043	ENST00000783576.1 link	n.355+643T>G	intron_variant	Intron 2 of 4
ENSG00000302043	ENST00000783577.1 link	n.203+11673T>G	intron_variant	Intron 1 of 2
ENSG00000302043	ENST00000783578.1 link	n.301+643T>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0623

AC:

9474

AN:

152116

Hom.:

404

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0279

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.0459

Gnomad ASJ

AF:

0.0225

Gnomad EAS

AF:

0.00926

Gnomad SAS

AF:

0.0193

Gnomad FIN

AF:

0.0526

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0958

Gnomad OTH

AF:

0.0488

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

GnomAD4 genome

AF:

0.0623

AC:

9490

AN:

152234

Hom.:

410

Cov.:

AF XY:

0.0575

AC XY:

4280

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0283

AC:

1177

AN:

41534

American (AMR)

AF:

0.0458

AC:

701

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0225

AC:

AN:

3468

East Asian (EAS)

AF:

0.00947

AC:

AN:

5172

South Asian (SAS)

AF:

0.0191

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0526

AC:

559

AN:

10624

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0958

AC:

6515

AN:

68008

Other (OTH)

AF:

0.0482

AC:

102

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

447

894

1342

1789

2236

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0838

Hom.:

1778

Bravo

AF:

0.0609

Asia WGS

AF:

0.0310

AC:

107

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.85

(source)

DANN

Benign

0.61

PhyloP100

-0.20

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