dbSNP rs2208713: ENSG00000293066:n.211-9751A>G (chr6-39970341-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 ENST00000649703.2(ENSG00000293066):n.211-9751A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 152,218 control chromosomes in the GnomAD database, including 548 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 0.061 ( 548 hom., cov: 32)

Consequence

ENSG00000293066
ENST00000649703.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293066 (HGNC:):

ENSG00000293066 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=-1.05).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723789	XR_001744112.1 link	n.260-4379A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000293066	ENST00000649703.2 link	n.211-9751A>G	intron_variant	Intron 3 of 4
ENSG00000293066	ENST00000741538.1 link	n.257-9751A>G	intron_variant	Intron 3 of 5
ENSG00000293066	ENST00000741539.1 link	n.153+6782A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0613

AC:

9328

AN:

152100

Hom.:

546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0762

Gnomad ASJ

AF:

0.0265

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.0303

Gnomad FIN

AF:

0.00584

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0190

Gnomad OTH

AF:

0.0709

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

GnomAD4 genome

AF:

0.0614

AC:

9344

AN:

152218

Hom.:

548

Cov.:

AF XY:

0.0610

AC XY:

4543

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.139

AC:

5758

AN:

41514

American (AMR)

AF:

0.0764

AC:

1168

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0265

AC:

AN:

3466

East Asian (EAS)

AF:

0.127

AC:

657

AN:

5178

South Asian (SAS)

AF:

0.0303

AC:

146

AN:

4816

European-Finnish (FIN)

AF:

0.00584

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0190

AC:

1295

AN:

68018

Other (OTH)

AF:

0.0707

AC:

149

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

416

831

1247

1662

2078

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0426

Hom.:

132

Bravo

AF:

0.0701

Asia WGS

AF:

0.0730

AC:

253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.69

(source)

DANN

Benign

0.34

PhyloP100

-2.3

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