4-186491213-G-C

Position:

• chr4-186491213-G-C

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+9632C>G 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 0.196 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: F11-AS1 NR_033900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

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=-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/exons	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.214+9632C>G		intron_variant, non_coding_transcript_variant
F11-AS1	NR_033901.2	n.214+9632C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F11-AS1	ENST00000505103.5	n.153+9632C>G		intron_variant, non_coding_transcript_variant		1
F11-AS1	ENST00000508110.5	n.153+9632C>G		intron_variant, non_coding_transcript_variant		5
F11-AS1	ENST00000508287.1	n.153+9632C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.172

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs713224; hg19: chr4-187412367;