dbSNP rs10511574: ENSG00000285784:n.388+23265A>C (chr9-11951204-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 ENST00000649122.1(ENSG00000285784):n.388+23265A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0504 in 151,970 control chromosomes in the GnomAD database, including 367 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 0.050 ( 367 hom., cov: 32)

Consequence

ENSG00000285784
ENST00000649122.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

6 publications found

Variant links:

Genes affected

ENSG00000285784 (HGNC:):

ENSG00000285784 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 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
ENSG00000285784	ENST00000649122.1 link	n.388+23265A>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.0504

AC:

7651

AN:

151854

Hom.:

367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0564

Gnomad AMI

AF:

0.0714

Gnomad AMR

AF:

0.0356

Gnomad ASJ

AF:

0.0591

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.0308

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0356

Gnomad OTH

AF:

0.0483

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

GnomAD4 genome

AF:

0.0504

AC:

7654

AN:

151970

Hom.:

367

Cov.:

AF XY:

0.0529

AC XY:

3929

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.0565

AC:

2334

AN:

41342

American (AMR)

AF:

0.0355

AC:

542

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0591

AC:

205

AN:

3470

East Asian (EAS)

AF:

0.180

AC:

924

AN:

5144

South Asian (SAS)

AF:

0.149

AC:

718

AN:

4816

European-Finnish (FIN)

AF:

0.0308

AC:

327

AN:

10620

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0356

AC:

2422

AN:

67998

Other (OTH)

AF:

0.0478

AC:

101

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

351

702

1054

1405

1756

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0395

Hom.:

123

Bravo

AF:

0.0512

Asia WGS

AF:

0.120

AC:

416

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.8

(source)

DANN

Benign

0.57

PhyloP100

0.35

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