ENST00000502457.1:n.295+564G>A

Variant names:

• chr5-44395913-G-A
• rs723166
• ENST00000502457.1:n.295+564G>A

Variant summary

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

The ENST00000502457.1(FGF10-AS1):​n.295+564G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,822 control chromosomes in the GnomAD database, including 4,548 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 0.22 (4548 hom., cov: 32)
• Consequence: FGF10-AS1 ENST00000502457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 4 publications found

Genes affected

FGF10-AS1 (HGNC:49382): (FGF10 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF10-AS1	NR_108034.1	n.295+564G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF10-AS1	ENST00000502457.1	n.295+564G>A		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33856 AN: 151706 Hom.: 4543 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.223 AC: 33874 AN: 151822 Hom.: 4548 Cov.: 32 AF XY: 0.225 AC XY: 16685 AN XY: 74182

African (AFR) AF: 0.0725 AC: 3003 AN: 41422

American (AMR) AF: 0.282 AC: 4304 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3464

East Asian (EAS) AF: 0.146 AC: 754 AN: 5152

South Asian (SAS) AF: 0.315 AC: 1515 AN: 4804

European-Finnish (FIN) AF: 0.357 AC: 3752 AN: 10498

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19079 AN: 67916

Other (OTH) AF: 0.232 AC: 490 AN: 2112

Alfa AF: 0.270 Hom.: 10949

Bravo AF: 0.209

Asia WGS AF: 0.294 AC: 1020 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.70
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs723166; hg19: chr5-44396015;