dbSNP rs11753837: ENSG00000291336:n.999+66348G>A (chr6-26190519-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000707189.1(ENSG00000291336):n.999+66348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,126 control chromosomes in the GnomAD database, including 911 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 ( 911 hom., cov: 31)

Consequence

ENSG00000291336
ENST00000707189.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580

Publications

17 publications found

Variant links:

Genes affected

ENSG00000291336 (HGNC:):

ENSG00000291336 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) 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
ENSG00000291336	ENST00000707189.1 link	n.999+66348G>A		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1 link	n.1000+32398G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16118

AN:

152008

Hom.:

914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.0851

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.0522

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.0970

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.106

AC:

16126

AN:

152126

Hom.:

911

Cov.:

AF XY:

0.107

AC XY:

7940

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.129

AC:

5363

AN:

41478

American (AMR)

AF:

0.0850

AC:

1300

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0706

AC:

245

AN:

3472

East Asian (EAS)

AF:

0.0527

AC:

273

AN:

5178

South Asian (SAS)

AF:

0.153

AC:

740

AN:

4822

European-Finnish (FIN)

AF:

0.117

AC:

1239

AN:

10578

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0971

AC:

6600

AN:

67992

Other (OTH)

AF:

0.108

AC:

227

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

746

1492

2239

2985

3731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<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:

0.100

Hom.:

1328

Bravo

AF:

0.103

Asia WGS

AF:

0.0890

AC:

308

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.71

(source)

DANN

Benign

0.26

PhyloP100

-0.058

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