dbSNP rs10514688: ENSG00000294886:n.222+91T>C (chr3-34921177-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 ENST00000726556.1(ENSG00000294886):n.222+91T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,268 control chromosomes in the GnomAD database, including 1,124 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 ( 1124 hom., cov: 33)

Consequence

ENSG00000294886
ENST00000726556.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.995

Publications

9 publications found

Variant links:

Genes affected

ENSG00000294886 (HGNC:):

ENSG00000294886 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=-0.57).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928135	NR_110817.1 link	n.207-41711A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000294886	ENST00000726556.1 link	n.222+91T>C	intron_variant	Intron 1 of 1
ENSG00000294861	ENST00000726394.1 link	n.-133A>G	upstream_gene_variant
ENSG00000294861	ENST00000726395.1 link	n.-180A>G	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17649

AN:

152150

Hom.:

1118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0941

Gnomad AMI

AF:

0.0815

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.0798

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.110

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

GnomAD4 genome

AF:

0.116

AC:

17672

AN:

152268

Hom.:

1124

Cov.:

AF XY:

0.118

AC XY:

8822

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0941

AC:

3911

AN:

41554

American (AMR)

AF:

0.115

AC:

1766

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0798

AC:

277

AN:

3470

East Asian (EAS)

AF:

0.175

AC:

905

AN:

5180

South Asian (SAS)

AF:

0.156

AC:

752

AN:

4834

European-Finnish (FIN)

AF:

0.152

AC:

1617

AN:

10606

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.119

AC:

8115

AN:

68012

Other (OTH)

AF:

0.110

AC:

233

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

787

1574

2362

3149

3936

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.119

Hom.:

3847

Bravo

AF:

0.113

Asia WGS

AF:

0.166

AC:

577

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

0.99

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