rs11931790

Variant names:

• chr4-186419534-C-T
• rs11931790
• ENST00000505103.5:n.153+81311G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 3 publications found

Genes affected

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

ENSG00000300494 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505103.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	NR_033900.1		n.214+81311G>A		intron	N/A
	F11-AS1	NR_033901.2		n.1573-3198G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	ENST00000505103.5	TSL:1	n.153+81311G>A		intron	N/A
	F11-AS1	ENST00000657917.1		n.347-40874G>A		intron	N/A
	F11-AS1	ENST00000771881.1		n.193-39112G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33757 AN: 151820 Hom.: 3835 Cov.: 32

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.: 32 AF XY: 0.219 AC XY: 16243 AN XY: 74280

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: 85 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16271 AN: 67952

Other (OTH) AF: 0.219 AC: 462 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.30
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs11931790; hg19: chr4-187340688;