dbSNP rs11627720: ENSG00000308787:n.126+10294A>C (chr14-42124332-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000836359.1(ENSG00000308787):n.126+10294A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,126 control chromosomes in the GnomAD database, including 1,504 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 0.12 ( 1504 hom., cov: 32)

Consequence

ENSG00000308787
ENST00000836359.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.27

Publications

1 publications found

Variant links:

Genes affected

ENSG00000308787 (HGNC:):

ENSG00000308787 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 (EAS) allele frequency at 95% confidence interval = 0.226 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
ENSG00000308787	ENST00000836359.1 link	n.126+10294A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18143

AN:

152008

Hom.:

1494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.0485

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.0658

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0574

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0608

Gnomad OTH

AF:

0.114

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

GnomAD4 genome

AF:

0.119

AC:

18176

AN:

152126

Hom.:

1504

Cov.:

AF XY:

0.121

AC XY:

8971

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.213

AC:

8845

AN:

41474

American (AMR)

AF:

0.144

AC:

2195

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0658

AC:

228

AN:

3466

East Asian (EAS)

AF:

0.237

AC:

1221

AN:

5160

South Asian (SAS)

AF:

0.127

AC:

613

AN:

4820

European-Finnish (FIN)

AF:

0.0574

AC:

608

AN:

10594

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0608

AC:

4133

AN:

68010

Other (OTH)

AF:

0.121

AC:

255

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

807

1614

2420

3227

4034

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.0777

Hom.:

314

Bravo

AF:

0.128

Asia WGS

AF:

0.224

AC:

781

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

5.1

(source)

DANN

Benign

0.79

PhyloP100

1.3

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