4-186305519-C-T

Position:

• chr4-186305519-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

F11-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.215-14487G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-14487G>A		intron_variant		1

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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.623

Alfa AF: 0.615 Hom.: 42761

Bravo AF: 0.567

Asia WGS AF: 0.756 AC: 2627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008728; hg19: chr4-187226673;