dbSNP rs566469: ENSG00000253634:n.720+266C>T (chr8-92502094-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 ENST00000648652.1(ENSG00000253634):n.720+266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,880 control chromosomes in the GnomAD database, including 2,695 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 0.16 ( 2695 hom., cov: 32)

Consequence

ENSG00000253634
ENST00000648652.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

1 publications found

Variant links:

Genes affected

ENSG00000253634 (HGNC:):

ENSG00000253634 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375639	XR_007061005.1 link	n.258+266C>T		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000253634	ENST00000648652.1 link	n.720+266C>T	intron_variant	Intron 6 of 13
ENSG00000253634	ENST00000744168.1 link	n.230+266C>T	intron_variant	Intron 3 of 6
ENSG00000253634	ENST00000744169.1 link	n.233+266C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24429

AN:

151762

Hom.:

2687

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.0901

Gnomad ASJ

AF:

0.0898

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0956

Gnomad OTH

AF:

0.155

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

GnomAD4 genome

AF:

0.161

AC:

24462

AN:

151880

Hom.:

2695

Cov.:

AF XY:

0.160

AC XY:

11891

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.302

AC:

12516

AN:

41404

American (AMR)

AF:

0.0899

AC:

1367

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.0898

AC:

311

AN:

3462

East Asian (EAS)

AF:

0.297

AC:

1532

AN:

5156

South Asian (SAS)

AF:

0.116

AC:

559

AN:

4820

European-Finnish (FIN)

AF:

0.103

AC:

1089

AN:

10572

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0957

AC:

6501

AN:

67944

Other (OTH)

AF:

0.154

AC:

326

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

993

1985

2978

3970

4963

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.129

Hom.:

956

Bravo

AF:

0.167

Asia WGS

AF:

0.210

AC:

731

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.69

(source)

DANN

Benign

0.43

PhyloP100

-1.4

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