dbSNP rs8092360: ENSG00000299452:n.826C>T (chr18-63106605-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000763649.1(ENSG00000299452):n.826C>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 0.25 in 152,088 control chromosomes in the GnomAD database, including 4,923 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 0.25 ( 4923 hom., cov: 32)

Consequence

ENSG00000299452
ENST00000763649.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.262

Publications

6 publications found

Variant links:

Genes affected

ENSG00000299452 (HGNC:):

ENSG00000299452 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299452	ENST00000763649.1 link	n.826C>T	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000299452	ENST00000763645.1 link	n.515+16168C>T	intron_variant	Intron 2 of 2
ENSG00000299452	ENST00000763648.1 link	n.499-5563C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37986

AN:

151970

Hom.:

4919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.250

AC:

38018

AN:

152088

Hom.:

4923

Cov.:

AF XY:

0.251

AC XY:

18665

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.332

AC:

13775

AN:

41468

American (AMR)

AF:

0.186

AC:

2845

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

1220

AN:

3470

East Asian (EAS)

AF:

0.266

AC:

1380

AN:

5186

South Asian (SAS)

AF:

0.284

AC:

1370

AN:

4820

European-Finnish (FIN)

AF:

0.251

AC:

2646

AN:

10552

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

13979

AN:

67990

Other (OTH)

AF:

0.243

AC:

512

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1444

2889

4333

5778

7222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.221

Hom.:

16466

Bravo

AF:

0.247

Asia WGS

AF:

0.242

AC:

843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.7

(source)

DANN

Benign

0.45

PhyloP100

-0.26

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