rs13133050

Variant names:

• chr4-186309583-A-C
• rs13133050
• ENST00000505103.5:n.154-18551T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-186309583-A-C
• chr4-186309583-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505103.5(F11-AS1):​n.154-18551T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,948 control chromosomes in the GnomAD database, including 28,068 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 0.58 (28068 hom., cov: 31)
• Consequence: F11-AS1 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.215-18551T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-18551T>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88111 AN: 151830 Hom.: 28078 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.580 AC: 88116 AN: 151948 Hom.: 28068 Cov.: 31 AF XY: 0.587 AC XY: 43566 AN XY: 74278

African (AFR) AF: 0.300 AC: 12440 AN: 41418

American (AMR) AF: 0.595 AC: 9080 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2380 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4432 AN: 5154

South Asian (SAS) AF: 0.819 AC: 3935 AN: 4802

European-Finnish (FIN) AF: 0.702 AC: 7409 AN: 10548

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46264 AN: 67968

Other (OTH) AF: 0.620 AC: 1311 AN: 2114

Alfa AF: 0.638 Hom.: 96886

Bravo AF: 0.555

Asia WGS AF: 0.790 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs13133050; hg19: chr4-187230737;