dbSNP rs11696364: ENSG00000286787:n.315G>T (chr20-1031383-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 ENST00000778971.1(ENSG00000286787):n.315G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 152,202 control chromosomes in the GnomAD database, including 315 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 0.054 ( 315 hom., cov: 32)

Consequence

ENSG00000286787
ENST00000778971.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260

Publications

5 publications found

Variant links:

Genes affected

ENSG00000286787 (HGNC:):

ENSG00000286787 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286787	ENST00000778971.1 link	n.315G>T	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000286787	ENST00000664648.2 link	n.352+1G>T	splice_donor_variant, intron_variant	Intron 3 of 3
ENSG00000301438	ENST00000778881.1 link	n.216+18979C>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0539

AC:

8194

AN:

152084

Hom.:

315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0154

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0391

Gnomad ASJ

AF:

0.0260

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0132

Gnomad FIN

AF:

0.0885

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0836

Gnomad OTH

AF:

0.0506

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

GnomAD4 genome

AF:

0.0538

AC:

8190

AN:

152202

Hom.:

315

Cov.:

AF XY:

0.0520

AC XY:

3870

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0154

AC:

638

AN:

41538

American (AMR)

AF:

0.0390

AC:

596

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0260

AC:

AN:

3468

East Asian (EAS)

AF:

0.000772

AC:

AN:

5182

South Asian (SAS)

AF:

0.0128

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0885

AC:

937

AN:

10588

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0836

AC:

5682

AN:

68006

Other (OTH)

AF:

0.0501

AC:

106

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

390

780

1171

1561

1951

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<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:

0.0649

Hom.:

824

Bravo

AF:

0.0492

Asia WGS

AF:

0.00953

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.7

(source)

DANN

Benign

0.63

PhyloP100

0.026

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