rs11132389

Positions:

• chr4-186330706-A-G
• chr4-186330706-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.215-39674T>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 0.398 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 NR_033900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.215-39674T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-39674T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000660474.1	n.77-4170A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.394

Alfa AF: 0.396 Hom.: 24636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11132389; hg19: chr4-187251860;