rs2889188

chr4-186394657-A-Gchr4-186394657-A-T

Variant summary

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

The NR_033900.1(F11-AS1):n.215-103625T>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 0.294 in 152,102 control chromosomes in the GnomAD database, including 7,544 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 0.29 (7544 hom., cov: 32)
• Consequence: F11-AS1 NR_033900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F11-AS1	NR_033900.1	n.215-103625T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-103625T>C		intron_variant, non_coding_transcript_variant		1
F11-AS1	ENST00000657917.1	n.347-15997T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44692 AN: 151984 Hom.: 7520 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.294 AC: 44772 AN: 152102 Hom.: 7544 Cov.: 32 AF XY: 0.287 AC XY: 21300 AN XY: 74344

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.295

Alfa AF: 0.253 Hom.: 10465

Bravo AF: 0.310

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.9
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2889188; hg19: chr4-187315811;