dbSNP rs963335: ENSG00000285520:n.510+4455C>G (chr10-12882659-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000649832.1(ENSG00000285520):n.510+4455C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,140 control chromosomes in the GnomAD database, including 3,176 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 0.13 ( 3176 hom., cov: 32)

Consequence

ENSG00000285520
ENST00000649832.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.177

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285520 (HGNC:):

ENSG00000285520 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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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
ENSG00000285520	ENST00000649832.1 link	n.510+4455C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19264

AN:

152022

Hom.:

3164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.384

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0623

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.0307

Gnomad FIN

AF:

0.0362

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0225

Gnomad OTH

AF:

0.116

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

GnomAD4 genome

AF:

0.127

AC:

19323

AN:

152140

Hom.:

3176

Cov.:

AF XY:

0.123

AC XY:

9181

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.384

AC:

15940

AN:

41472

American (AMR)

AF:

0.0622

AC:

950

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3470

East Asian (EAS)

AF:

0.00193

AC:

AN:

5184

South Asian (SAS)

AF:

0.0299

AC:

144

AN:

4820

European-Finnish (FIN)

AF:

0.0362

AC:

383

AN:

10572

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0225

AC:

1531

AN:

68022

Other (OTH)

AF:

0.117

AC:

248

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

688

1376

2063

2751

3439

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.00754

Hom.:

Bravo

AF:

0.140

Asia WGS

AF:

0.0500

AC:

173

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.95

(source)

DANN

Benign

0.29

PhyloP100

0.18

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