rs13148903

Variant names:

• chr4-186336422-A-G
• rs13148903
• ENST00000505103.5:n.154-45390T>C

Variant summary

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

The ENST00000505103.5(F11-AS1):​n.154-45390T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,204 control chromosomes in the GnomAD database, including 3,225 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 0.20 (3225 hom., cov: 33)
• Consequence: F11-AS1 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 3 publications found

Genes affected

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

ENSG00000287667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.215-45390T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-45390T>C		intron_variant	Intron 1 of 3	1
ENSG00000287667	ENST00000660474.1	n.1623A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29688 AN: 152086 Hom.: 3220 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0778

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.195 AC: 29713 AN: 152204 Hom.: 3225 Cov.: 33 AF XY: 0.194 AC XY: 14407 AN XY: 74450

African (AFR) AF: 0.111 AC: 4601 AN: 41526

American (AMR) AF: 0.190 AC: 2899 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3470

East Asian (EAS) AF: 0.0777 AC: 403 AN: 5184

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4830

European-Finnish (FIN) AF: 0.212 AC: 2251 AN: 10612

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17237 AN: 67988

Other (OTH) AF: 0.212 AC: 446 AN: 2106

Alfa AF: 0.224 Hom.: 11317

Bravo AF: 0.187

Asia WGS AF: 0.144 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs13148903; hg19: chr4-187257576;