dbSNP rs7755450: ENSG00000286680:n.131+20403C>T (chr6-67909510-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 ENST00000653528.1(ENSG00000286680):n.131+20403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,206 control chromosomes in the GnomAD database, including 413 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 0.058 ( 413 hom., cov: 32)

Consequence

ENSG00000286680
ENST00000653528.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286680 (HGNC:):

ENSG00000286680 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377845	XR_942662.1 link	n.909-11941C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286680	ENST00000653528.1 link	n.131+20403C>T	intron_variant	Intron 1 of 3
ENSG00000286680	ENST00000661401.1 link	n.121-11941C>T	intron_variant	Intron 2 of 3
ENSG00000286680	ENST00000718119.1 link	n.154-11941C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0578

AC:

8798

AN:

152088

Hom.:

410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.0292

Gnomad ASJ

AF:

0.0216

Gnomad EAS

AF:

0.0133

Gnomad SAS

AF:

0.0130

Gnomad FIN

AF:

0.0263

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0377

Gnomad OTH

AF:

0.0446

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

GnomAD4 genome

AF:

0.0579

AC:

8806

AN:

152206

Hom.:

413

Cov.:

AF XY:

0.0552

AC XY:

4107

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.124

AC:

5140

AN:

41526

American (AMR)

AF:

0.0292

AC:

446

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0216

AC:

AN:

3472

East Asian (EAS)

AF:

0.0135

AC:

AN:

5178

South Asian (SAS)

AF:

0.0128

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0263

AC:

279

AN:

10610

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0377

AC:

2562

AN:

67986

Other (OTH)

AF:

0.0441

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

411

822

1233

1644

2055

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:

0.0462

Hom.:

338

Bravo

AF:

0.0608

Asia WGS

AF:

0.0230

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.0

(source)

DANN

Benign

0.68

PhyloP100

-0.11

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