4-186417181-C-T

Position:

• chr4-186417181-C-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.214+83664G>A 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 0.263 in 152,206 control chromosomes in the GnomAD database, including 5,413 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 0.26 (5413 hom., cov: 32)
• Consequence: F11-AS1 NR_033900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F11-AS1	NR_033900.1	n.214+83664G>A		intron_variant, non_coding_transcript_variant
F11-AS1	NR_033901.2	n.1573-845G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F11-AS1	ENST00000505103.5	n.153+83664G>A		intron_variant, non_coding_transcript_variant		1
F11-AS1	ENST00000657917.1	n.347-38521G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39977 AN: 152088 Hom.: 5411 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.263 AC: 40005 AN: 152206 Hom.: 5413 Cov.: 32 AF XY: 0.263 AC XY: 19539 AN XY: 74404

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.272

Alfa AF: 0.267 Hom.: 4938

Bravo AF: 0.253

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.96
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11935103; hg19: chr4-187338335;