dbSNP rs7133541: ENSG00000288729:n.163-11870C>T (chr12-3935310-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 ENST00000687881.2(ENSG00000288729):n.163-11870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 149,200 control chromosomes in the GnomAD database, including 11,680 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 0.36 ( 11680 hom., cov: 31)

Consequence

ENSG00000288729
ENST00000687881.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Publications

1 publications found

Variant links:

Genes affected

ENSG00000288729 (HGNC:):

ENSG00000288729 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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369608	XR_931557.4 link	n.161-11870C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288729	ENST00000687881.2 link	n.163-11870C>T	intron_variant	Intron 2 of 2
ENSG00000288729	ENST00000690597.1 link	n.273-11870C>T	intron_variant	Intron 3 of 3
ENSG00000288729	ENST00000701907.2 link	n.165+21422C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

53853

AN:

149100

Hom.:

11658

Cov.:

show subpopulations

Gnomad AFR

AF:

0.431

Gnomad AMI

AF:

0.394

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.392

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

GnomAD4 genome

AF:

0.361

AC:

53915

AN:

149200

Hom.:

11680

Cov.:

AF XY:

0.363

AC XY:

26433

AN XY:

72794

show subpopulations

African (AFR)

AF:

0.432

AC:

17218

AN:

39876

American (AMR)

AF:

0.372

AC:

5484

AN:

14738

Ashkenazi Jewish (ASJ)

AF:

0.412

AC:

1425

AN:

3458

East Asian (EAS)

AF:

0.203

AC:

1009

AN:

4966

South Asian (SAS)

AF:

0.434

AC:

2032

AN:

4678

European-Finnish (FIN)

AF:

0.306

AC:

3203

AN:

10462

Middle Eastern (MID)

AF:

0.545

AC:

158

AN:

290

European-Non Finnish (NFE)

AF:

0.328

AC:

22211

AN:

67764

Other (OTH)

AF:

0.397

AC:

818

AN:

2062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1568

3136

4703

6271

7839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<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:

0.347

Hom.:

9041

Asia WGS

AF:

0.409

AC:

1386

AN:

3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.73

(source)

DANN

Benign

0.40

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