dbSNP rs11119132: ENSG00000293786:n.315+2532G>T (chr1-208819087-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000718977.1(ENSG00000293786):n.315+2532G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 152,212 control chromosomes in the GnomAD database, including 286 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 0.049 ( 286 hom., cov: 32)

Consequence

ENSG00000293786
ENST00000718977.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.631

Publications

2 publications found

Variant links:

Genes affected

ENSG00000293786 (HGNC:):

ENSG00000293786 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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0729 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
ENSG00000293786	ENST00000718977.1 link	n.315+2532G>T		intron_variant	Intron 3 of 3
ENSG00000293786	ENST00000718978.1 link	n.159-303G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0493

AC:

7494

AN:

152094

Hom.:

287

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0154

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.0376

Gnomad ASJ

AF:

0.0208

Gnomad EAS

AF:

0.0494

Gnomad SAS

AF:

0.0222

Gnomad FIN

AF:

0.0535

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0747

Gnomad OTH

AF:

0.0407

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

GnomAD4 genome

AF:

0.0492

AC:

7494

AN:

152212

Hom.:

286

Cov.:

AF XY:

0.0474

AC XY:

3526

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.0153

AC:

636

AN:

41548

American (AMR)

AF:

0.0376

AC:

575

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0208

AC:

AN:

3468

East Asian (EAS)

AF:

0.0494

AC:

255

AN:

5166

South Asian (SAS)

AF:

0.0220

AC:

106

AN:

4824

European-Finnish (FIN)

AF:

0.0535

AC:

566

AN:

10578

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0747

AC:

5078

AN:

68020

Other (OTH)

AF:

0.0421

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

366

732

1099

1465

1831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<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:

0.0324

Hom.:

Bravo

AF:

0.0477

Asia WGS

AF:

0.0380

AC:

132

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.59

PhyloP100

0.63

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