chr4-186296484-A-G

Variant names:

• chr4-186296484-A-G
• rs12500151
• ENST00000505103.5:n.154-5452T>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.154-5452T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,192 control chromosomes in the GnomAD database, including 4,254 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 (4254 hom., cov: 32)
• Consequence: F11-AS1 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 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.215-5452T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	ENST00000505103.5	TSL:1	n.154-5452T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33282 AN: 152074 Hom.: 4250 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.219 AC: 33307 AN: 152192 Hom.: 4254 Cov.: 32 AF XY: 0.216 AC XY: 16072 AN XY: 74400

African (AFR) AF: 0.100 AC: 4172 AN: 41546

American (AMR) AF: 0.227 AC: 3474 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3472

East Asian (EAS) AF: 0.135 AC: 698 AN: 5176

South Asian (SAS) AF: 0.251 AC: 1205 AN: 4806

European-Finnish (FIN) AF: 0.202 AC: 2136 AN: 10586

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19504 AN: 67984

Other (OTH) AF: 0.234 AC: 496 AN: 2116

Alfa AF: 0.277 Hom.: 2864

Bravo AF: 0.216

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.78
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs12500151; hg19: chr4-187217638;