rs10473354

Variant names:

• chr5-44396251-A-G
• rs10473354
• ENST00000502457.1:n.295+902A>G

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+902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 145,192 control chromosomes in the GnomAD database, including 9,047 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 0.35 (9047 hom., cov: 30)
• Consequence: FGF10-AS1 ENST00000502457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF10-AS1	NR_108034.1	n.295+902A>G		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+902A>G		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 51085 AN: 145144 Hom.: 9046 Cov.: 30

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.352 AC: 51109 AN: 145192 Hom.: 9047 Cov.: 30 AF XY: 0.353 AC XY: 24931 AN XY: 70646

African (AFR) AF: 0.242 AC: 9155 AN: 37756

American (AMR) AF: 0.408 AC: 6039 AN: 14810

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1209 AN: 3408

East Asian (EAS) AF: 0.461 AC: 2338 AN: 5074

South Asian (SAS) AF: 0.282 AC: 1313 AN: 4654

European-Finnish (FIN) AF: 0.347 AC: 3321 AN: 9560

Middle Eastern (MID) AF: 0.375 AC: 108 AN: 288

European-Non Finnish (NFE) AF: 0.395 AC: 26361 AN: 66706

Other (OTH) AF: 0.373 AC: 761 AN: 2040

Alfa AF: 0.307 Hom.: 1539

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10473354; hg19: chr5-44396353;