rs10473354

chr5-44396251-A-G

Variant summary

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

The NR_108034.1(FGF10-AS1):n.295+902A>G variant causes a intron, non coding transcript 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 NR_108034.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FGF10-AS1	NR_108034.1	n.295+902A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF10-AS1	ENST00000502457.1	n.295+902A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.373

Alfa AF: 0.354 Hom.: 1000

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10473354; hg19: chr5-44396353;