4-186491213-G-C

Variant names:

• chr4-186491213-G-C
• rs713224
• ENST00000509111.2:c.145+63969C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509111.2(ENSG00000272297):​c.145+63969C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,640 control chromosomes in the GnomAD database, including 3,726 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 0.20 (3726 hom., cov: 32)
• Consequence: ENSG00000272297 ENST00000509111.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 3 publications found

Genes affected

ENSG00000272297 (HGNC:):

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.214+9632C>G		intron_variant	Intron 1 of 3
F11-AS1	NR_033901.2	n.214+9632C>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272297	ENST00000509111.2	c.145+63969C>G		intron_variant	Intron 1 of 1	3		ENSP00000422449.2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29707 AN: 151522 Hom.: 3722 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.196 AC: 29719 AN: 151640 Hom.: 3726 Cov.: 32 AF XY: 0.198 AC XY: 14671 AN XY: 74078

African (AFR) AF: 0.0798 AC: 3300 AN: 41348

American (AMR) AF: 0.251 AC: 3820 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3462

East Asian (EAS) AF: 0.517 AC: 2649 AN: 5122

South Asian (SAS) AF: 0.294 AC: 1407 AN: 4788

European-Finnish (FIN) AF: 0.226 AC: 2371 AN: 10474

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15141 AN: 67908

Other (OTH) AF: 0.172 AC: 362 AN: 2108

Alfa AF: 0.104 Hom.: 179

Bravo AF: 0.194

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.48
PhyloP100		-0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs713224; hg19: chr4-187412367;