Genetic Variant ENSG00000302734:n.1103-2262C>T (chr6-12298751-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 ENST00000789274.1(ENSG00000302734):n.1103-2262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,144 control chromosomes in the GnomAD database, including 8,685 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 0.30 ( 8685 hom., cov: 33)

Consequence

ENSG00000302734
ENST00000789274.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.32

Publications

10 publications found

Variant links:

Genes affected

ENSG00000302734 (HGNC:):

ENSG00000302734 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000302734	ENST00000789274.1 link	n.1103-2262C>T	intron_variant	Intron 1 of 1
ENSG00000302734	ENST00000789275.1 link	n.704-2262C>T	intron_variant	Intron 3 of 3
ENSG00000302734	ENST00000789276.1 link	n.1706-2262C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.298

AC:

45318

AN:

152026

Hom.:

8688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.380

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.377

Gnomad EAS

AF:

0.0385

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.429

Gnomad OTH

AF:

0.321

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

GnomAD4 genome

AF:

0.298

AC:

45308

AN:

152144

Hom.:

8685

Cov.:

AF XY:

0.295

AC XY:

21933

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0769

AC:

3192

AN:

41534

American (AMR)

AF:

0.312

AC:

4772

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.377

AC:

1306

AN:

3468

East Asian (EAS)

AF:

0.0386

AC:

200

AN:

5186

South Asian (SAS)

AF:

0.236

AC:

1140

AN:

4828

European-Finnish (FIN)

AF:

0.418

AC:

4408

AN:

10556

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.429

AC:

29172

AN:

67980

Other (OTH)

AF:

0.317

AC:

668

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1478

2955

4433

5910

7388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

460

920

1380

1840

2300

<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:

0.377

Hom.:

38262

Bravo

AF:

0.279

Asia WGS

AF:

0.126

AC:

439

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

9.9

(source)

DANN

Benign

0.69

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