4-186369953-G-A

Variant names:

• chr4-186369953-G-A
• rs13149354
• ENST00000505103.5:n.154-78921C>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.154-78921C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,788 control chromosomes in the GnomAD database, including 6,228 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 0.28 (6228 hom., cov: 31)
• Consequence: F11-AS1 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.333 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	NR_033900.1		n.215-78921C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	ENST00000505103.5	TSL:1	n.154-78921C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42352 AN: 151676 Hom.: 6222 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.279 AC: 42376 AN: 151788 Hom.: 6228 Cov.: 31 AF XY: 0.276 AC XY: 20458 AN XY: 74176

African (AFR) AF: 0.195 AC: 8065 AN: 41360

American (AMR) AF: 0.271 AC: 4129 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3468

East Asian (EAS) AF: 0.158 AC: 816 AN: 5168

South Asian (SAS) AF: 0.289 AC: 1385 AN: 4800

European-Finnish (FIN) AF: 0.276 AC: 2894 AN: 10488

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22850 AN: 67946

Other (OTH) AF: 0.309 AC: 651 AN: 2104

Alfa AF: 0.311 Hom.: 1514

Bravo AF: 0.275

Asia WGS AF: 0.236 AC: 821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs13149354; hg19: chr4-187291107;