4-186305519-C-T

Variant names:

• chr4-186305519-C-T
• rs1008728
• ENST00000505103.5:n.154-14487G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505103.5(F11-AS1):​n.154-14487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,168 control chromosomes in the GnomAD database, including 26,631 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 0.58 (26631 hom., cov: 34)
• Consequence: F11-AS1 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505103.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	NR_033900.1		n.215-14487G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	ENST00000505103.5	TSL:1	n.154-14487G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88434 AN: 152050 Hom.: 26636 Cov.: 34

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.581 AC: 88453 AN: 152168 Hom.: 26631 Cov.: 34 AF XY: 0.586 AC XY: 43609 AN XY: 74384

African (AFR) AF: 0.420 AC: 17443 AN: 41482

American (AMR) AF: 0.604 AC: 9240 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2057 AN: 3472

East Asian (EAS) AF: 0.806 AC: 4160 AN: 5162

South Asian (SAS) AF: 0.722 AC: 3478 AN: 4820

European-Finnish (FIN) AF: 0.662 AC: 7008 AN: 10594

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42993 AN: 68012

Other (OTH) AF: 0.623 AC: 1316 AN: 2114

Alfa AF: 0.611 Hom.: 62888

Bravo AF: 0.567

Asia WGS AF: 0.756 AC: 2627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.018
DANN	Benign	0.71
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1008728; hg19: chr4-187226673;