dbSNP rs6901830: ENSG00000291111:n.430-10554G>A (chr6-33130567-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 ENST00000782892.1(ENSG00000291111):n.430-10554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,174 control chromosomes in the GnomAD database, including 1,473 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 0.13 ( 1473 hom., cov: 32)

Consequence

ENSG00000291111
ENST00000782892.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

11 publications found

Variant links:

Genes affected

ENSG00000291111 (HGNC:):

ENSG00000291111 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=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1 link	n.*180C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291111	ENST00000782892.1 link	n.430-10554G>A	intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1 link	n.404-10554G>A	intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782894.1 link	n.229-678G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19860

AN:

152056

Hom.:

1477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0759

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.0951

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.117

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

GnomAD4 genome

AF:

0.131

AC:

19870

AN:

152174

Hom.:

1473

Cov.:

AF XY:

0.130

AC XY:

9641

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0762

AC:

3164

AN:

41536

American (AMR)

AF:

0.0951

AC:

1454

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.178

AC:

619

AN:

3470

East Asian (EAS)

AF:

0.134

AC:

691

AN:

5172

South Asian (SAS)

AF:

0.148

AC:

711

AN:

4820

European-Finnish (FIN)

AF:

0.177

AC:

1866

AN:

10570

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.162

AC:

11044

AN:

67990

Other (OTH)

AF:

0.116

AC:

246

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

889

1777

2666

3554

4443

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.148

Hom.:

3558

Bravo

AF:

0.120

Asia WGS

AF:

0.144

AC:

502

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.65

(source)

DANN

Benign

0.49

PhyloP100

-1.2

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