dbSNP rs2508049: ENSG00000290870:n.2155+1240T>C (chr6-29856106-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000647952.1(ENSG00000290870):n.2155+1240T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 150,404 control chromosomes in the GnomAD database, including 1,141 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 0.11 ( 1141 hom., cov: 33)

Consequence

ENSG00000290870
ENST00000647952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.876

Publications

14 publications found

Variant links:

Genes affected

ENSG00000290870 (HGNC:):

ENSG00000290870 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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375010	XR_926680.3 link	n.41+1240T>C	intron_variant	Intron 1 of 2
LOC105375010	XR_926681.2 link	n.41+1240T>C	intron_variant	Intron 1 of 3
LOC105375010	XR_926682.3 link	n.41+1240T>C	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1 link	n.2155+1240T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16130

AN:

150294

Hom.:

1140

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0362

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.0757

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.0196

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.0787

Gnomad MID

AF:

0.147

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.104

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

GnomAD4 genome

AF:

0.107

AC:

16132

AN:

150404

Hom.:

1141

Cov.:

AF XY:

0.103

AC XY:

7539

AN XY:

73510

show subpopulations

African (AFR)

AF:

0.0364

AC:

1492

AN:

41034

American (AMR)

AF:

0.0756

AC:

1127

AN:

14916

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

420

AN:

3432

East Asian (EAS)

AF:

0.0197

AC:

AN:

4976

South Asian (SAS)

AF:

0.131

AC:

616

AN:

4696

European-Finnish (FIN)

AF:

0.0787

AC:

827

AN:

10510

Middle Eastern (MID)

AF:

0.141

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.165

AC:

11139

AN:

67572

Other (OTH)

AF:

0.104

AC:

215

AN:

2072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

724

1448

2172

2896

3620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.141

Hom.:

3924

Bravo

AF:

0.101

Asia WGS

AF:

0.0670

AC:

237

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.6

(source)

DANN

Benign

0.17

PhyloP100

-0.88

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