dbSNP rs11200376: ENSG00000286876:n.87-29944C>T (chr10-83749657-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 ENST00000789038.1(ENSG00000286876):n.87-29944C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 152,150 control chromosomes in the GnomAD database, including 560 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 0.076 ( 560 hom., cov: 32)

Consequence

ENSG00000286876
ENST00000789038.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

Publications

2 publications found

Variant links:

Genes affected

ENSG00000286876 (HGNC:):

ENSG00000286876 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286876	ENST00000789038.1 link	n.87-29944C>T	intron_variant	Intron 1 of 2
ENSG00000286876	ENST00000789039.1 link	n.282+24249C>T	intron_variant	Intron 1 of 2
ENSG00000286876	ENST00000789040.1 link	n.54+9890C>T	intron_variant	Intron 1 of 2
ENSG00000286876	ENST00000789041.1 link	n.73+7902C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0760

AC:

11552

AN:

152032

Hom.:

561

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0211

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.0564

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.0937

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0980

Gnomad OTH

AF:

0.0585

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

GnomAD4 genome

AF:

0.0760

AC:

11558

AN:

152150

Hom.:

560

Cov.:

AF XY:

0.0769

AC XY:

5719

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.0210

AC:

873

AN:

41530

American (AMR)

AF:

0.0564

AC:

861

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.142

AC:

492

AN:

3464

East Asian (EAS)

AF:

0.107

AC:

552

AN:

5166

South Asian (SAS)

AF:

0.149

AC:

718

AN:

4824

European-Finnish (FIN)

AF:

0.0937

AC:

991

AN:

10578

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0980

AC:

6666

AN:

68000

Other (OTH)

AF:

0.0588

AC:

124

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

537

1075

1612

2150

2687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.0835

Hom.:

134

Bravo

AF:

0.0687

Asia WGS

AF:

0.0980

AC:

342

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.9

(source)

DANN

Benign

0.58

PhyloP100

0.25

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