4-186394657-A-G

Variant names:

• chr4-186394657-A-G
• rs2889188
• ENST00000505103.5:n.154-103625T>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.154-103625T>C variant causes a intron 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 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 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.215-103625T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	ENST00000505103.5	TSL:1	n.154-103625T>C		intron	N/A
	F11-AS1	ENST00000657917.1		n.347-15997T>C		intron	N/A
	F11-AS1	ENST00000771881.1		n.193-14235T>C		intron	N/A

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

African (AFR) AF: 0.461 AC: 19104 AN: 41474

American (AMR) AF: 0.246 AC: 3761 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3472

East Asian (EAS) AF: 0.137 AC: 708 AN: 5178

South Asian (SAS) AF: 0.144 AC: 694 AN: 4830

European-Finnish (FIN) AF: 0.172 AC: 1825 AN: 10586

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16772 AN: 67980

Other (OTH) AF: 0.295 AC: 621 AN: 2102

Alfa AF: 0.261 Hom.: 23698

Bravo AF: 0.310

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs2889188; hg19: chr4-187315811;