dbSNP rs9283878: ENSG00000303414:n.101C>T (chr6-26754842-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 ENST00000794331.1(ENSG00000303414):n.101C>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 0.0303 in 128,002 control chromosomes in the GnomAD database, including 289 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 0.030 ( 289 hom., cov: 22)

Consequence

ENSG00000303414
ENST00000794331.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.998

Publications

1 publications found

Variant links:

Genes affected

ENSG00000303414 (HGNC:):

ENSG00000303414 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0778 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
ENSG00000303414	ENST00000794331.1 link	n.101C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0302

AC:

3868

AN:

127908

Hom.:

288

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0801

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0222

Gnomad ASJ

AF:

0.0224

Gnomad EAS

AF:

0.0205

Gnomad SAS

AF:

0.00261

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0224

Gnomad NFE

AF:

0.00354

Gnomad OTH

AF:

0.0325

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

GnomAD4 genome

AF:

0.0303

AC:

3878

AN:

128002

Hom.:

289

Cov.:

AF XY:

0.0297

AC XY:

1847

AN XY:

62086

show subpopulations

African (AFR)

AF:

0.0801

AC:

3219

AN:

40206

American (AMR)

AF:

0.0222

AC:

274

AN:

12330

Ashkenazi Jewish (ASJ)

AF:

0.0224

AC:

AN:

2636

East Asian (EAS)

AF:

0.0205

AC:

AN:

2926

South Asian (SAS)

AF:

0.00261

AC:

AN:

3070

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8898

Middle Eastern (MID)

AF:

0.0242

AC:

AN:

248

European-Non Finnish (NFE)

AF:

0.00354

AC:

195

AN:

55124

Other (OTH)

AF:

0.0324

AC:

AN:

1758

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

179

269

358

448

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<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:

0.0182

Hom.:

Asia WGS

AF:

0.0140

AC:

AN:

2338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Uncertain

0.98

PhyloP100

1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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