rs13148903

Positions:

• chr4-186336422-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660474.1(ENSG00000287667):​n.1623A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,204 control chromosomes in the GnomAD database, including 3,225 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 (3225 hom., cov: 33)
• Consequence: ENST00000660474.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

(HGNC:):

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F11-AS1	NR_033900.1	n.215-45390T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660474.1	n.1623A>G		non_coding_transcript_exon_variant	2/2
F11-AS1	ENST00000505103.5	n.154-45390T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29688 AN: 152086 Hom.: 3220 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0778

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.195 AC: 29713 AN: 152204 Hom.: 3225 Cov.: 33 AF XY: 0.194 AC XY: 14407 AN XY: 74450

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0777

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.212

Alfa AF: 0.236 Hom.: 7696

Bravo AF: 0.187

Asia WGS AF: 0.144 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13148903; hg19: chr4-187257576;