chr4-186330706-A-G

Variant names:

• chr4-186330706-A-G
• rs11132389
• ENST00000505103.5:n.154-39674T>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.154-39674T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,306 control chromosomes in the GnomAD database, including 12,082 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 0.40 (12082 hom., cov: 32)
• Consequence: F11-AS1 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 9 publications found

Genes affected

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

ENSG00000287667 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.215-39674T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-39674T>C		intron_variant	Intron 1 of 3	1
ENSG00000287667	ENST00000660474.1	n.77-4170A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60107 AN: 151194 Hom.: 12074 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.398 AC: 60153 AN: 151306 Hom.: 12082 Cov.: 32 AF XY: 0.402 AC XY: 29691 AN XY: 73918

African (AFR) AF: 0.352 AC: 14519 AN: 41258

American (AMR) AF: 0.424 AC: 6466 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1227 AN: 3458

East Asian (EAS) AF: 0.637 AC: 3290 AN: 5164

South Asian (SAS) AF: 0.396 AC: 1895 AN: 4784

European-Finnish (FIN) AF: 0.482 AC: 4983 AN: 10338

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26649 AN: 67776

Other (OTH) AF: 0.394 AC: 824 AN: 2092

Alfa AF: 0.398 Hom.: 51310

Bravo AF: 0.396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.49
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs11132389; hg19: chr4-187251860;