dbSNP rs10507449: ENSG00000307651:n.233-15706T>C (chr13-37291646-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000827668.1(ENSG00000307651):n.233-15706T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 152,264 control chromosomes in the GnomAD database, including 152 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 0.034 ( 152 hom., cov: 33)

Consequence

ENSG00000307651
ENST00000827668.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.605

Publications

1 publications found

Variant links:

Genes affected

ENSG00000307651 (HGNC:):

ENSG00000307651 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 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
ENSG00000307651	ENST00000827668.1 link	n.233-15706T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0336

AC:

5107

AN:

152146

Hom.:

151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0321

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0627

Gnomad ASJ

AF:

0.0326

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.0424

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0190

Gnomad OTH

AF:

0.0392

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

GnomAD4 genome

AF:

0.0336

AC:

5114

AN:

152264

Hom.:

152

Cov.:

AF XY:

0.0348

AC XY:

2593

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.0321

AC:

1335

AN:

41564

American (AMR)

AF:

0.0627

AC:

959

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0326

AC:

113

AN:

3464

East Asian (EAS)

AF:

0.153

AC:

794

AN:

5182

South Asian (SAS)

AF:

0.0157

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0424

AC:

450

AN:

10612

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0190

AC:

1292

AN:

68000

Other (OTH)

AF:

0.0388

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

243

486

730

973

1216

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<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:

0.0263

Hom.:

173

Bravo

AF:

0.0370

Asia WGS

AF:

0.0850

AC:

297

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.45

(source)

DANN

Benign

0.53

PhyloP100

-0.60

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