rs1482680

Positions:

• chr5-44392040-G-A

Variant summary

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

The ENST00000502457.1(FGF10-AS1):​n.182+3127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,002 control chromosomes in the GnomAD database, including 23,313 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 0.52 (23313 hom., cov: 32)
• Consequence: FGF10-AS1 ENST00000502457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

Genes affected

FGF10-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF10-AS1	NR_108034.1	n.182+3127G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF10-AS1	ENST00000502457.1	n.182+3127G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78928 AN: 151880 Hom.: 23311 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.519 AC: 78950 AN: 152002 Hom.: 23313 Cov.: 32 AF XY: 0.523 AC XY: 38825 AN XY: 74296

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.540

Alfa AF: 0.581 Hom.: 8445

Bravo AF: 0.492

Asia WGS AF: 0.475 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1482680; hg19: chr5-44392142; COSMIC: COSV52934567;