dbSNP rs1004565: ENSG00000302828:n.65-39241G>A (chr11-79666656-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000789891.1(ENSG00000302828):n.65-39241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 152,234 control chromosomes in the GnomAD database, including 380 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 0.055 ( 380 hom., cov: 33)

Consequence

ENSG00000302828
ENST00000789891.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.155

Publications

1 publications found

Variant links:

Genes affected

ENSG00000302828 (HGNC:):

ENSG00000302828 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 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
ENSG00000302828	ENST00000789891.1 link	n.65-39241G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0548

AC:

8337

AN:

152116

Hom.:

381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0372

Gnomad ASJ

AF:

0.0461

Gnomad EAS

AF:

0.000579

Gnomad SAS

AF:

0.0493

Gnomad FIN

AF:

0.0155

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0252

Gnomad OTH

AF:

0.0566

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

GnomAD4 genome

AF:

0.0548

AC:

8343

AN:

152234

Hom.:

380

Cov.:

AF XY:

0.0533

AC XY:

3966

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.128

AC:

5326

AN:

41534

American (AMR)

AF:

0.0372

AC:

569

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0461

AC:

160

AN:

3472

East Asian (EAS)

AF:

0.000580

AC:

AN:

5170

South Asian (SAS)

AF:

0.0485

AC:

234

AN:

4820

European-Finnish (FIN)

AF:

0.0155

AC:

164

AN:

10606

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0251

AC:

1709

AN:

68022

Other (OTH)

AF:

0.0560

AC:

118

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

374

748

1123

1497

1871

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0402

Hom.:

Bravo

AF:

0.0589

Asia WGS

AF:

0.0280

AC:

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

1.6

(source)

DANN

Benign

0.35

PhyloP100

-0.15

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