dbSNP rs11931790: F11-AS1:n.153+81311G>A (chr4-186419534-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000505103.5(F11-AS1):n.153+81311G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,940 control chromosomes in the GnomAD database, including 3,836 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 0.22 ( 3836 hom., cov: 32)

Consequence

F11-AS1
ENST00000505103.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.427

Publications

3 publications found

Variant links:

Genes affected

F11-AS1 (HGNC:27725): (F11 antisense RNA 1)

F11-AS1 links:

ENSG00000300494 (HGNC:):

ENSG00000300494 links:

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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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F11-AS1	NR_033900.1 link	n.214+81311G>A		intron_variant	Intron 1 of 3
F11-AS1	NR_033901.2 link	n.1573-3198G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
F11-AS1	ENST00000505103.5 link	n.153+81311G>A	intron_variant	Intron 1 of 3	1
F11-AS1	ENST00000657917.1 link	n.347-40874G>A	intron_variant	Intron 1 of 1
F11-AS1	ENST00000771881.1 link	n.193-39112G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

33757

AN:

151820

Hom.:

3835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.0901

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.0843

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.222

AC:

33765

AN:

151940

Hom.:

3836

Cov.:

AF XY:

0.219

AC XY:

16243

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.226

AC:

9354

AN:

41412

American (AMR)

AF:

0.213

AC:

3258

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

728

AN:

3466

East Asian (EAS)

AF:

0.0848

AC:

439

AN:

5174

South Asian (SAS)

AF:

0.216

AC:

1037

AN:

4806

European-Finnish (FIN)

AF:

0.194

AC:

2049

AN:

10546

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16271

AN:

67952

Other (OTH)

AF:

0.219

AC:

462

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1341

2682

4023

5364

6705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.233

Hom.:

9304

Bravo

AF:

0.223

Asia WGS

AF:

0.149

AC:

520

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.24

(source)

DANN

Benign

0.30

PhyloP100

-0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs11931790

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