rs12500151

chr4-186296484-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033900.1(F11-AS1):n.215-5452T>C variant causes a intron, non coding transcript 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 NR_033900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F11-AS1	NR_033900.1	n.215-5452T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-5452T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.234

Alfa AF: 0.276 Hom.: 2471

Bravo AF: 0.216

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12500151; hg19: chr4-187217638;