5-44389924-T-C

Variant summary

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

The NR_108034.1(FGF10-AS1):n.182+1011T>C 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 0.969 in 151,766 control chromosomes in the GnomAD database, including 71,380 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 0.97 (71380 hom., cov: 28)
• Consequence: FGF10-AS1 NR_108034.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF10-AS1	NR_108034.1	n.182+1011T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF10-AS1	ENST00000502457.1	n.182+1011T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.969 AC: 146962 AN: 151648 Hom.: 71332 Cov.: 28

Gnomad AFR AF: 0.937

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.969 AC: 147069 AN: 151766 Hom.: 71380 Cov.: 28 AF XY: 0.967 AC XY: 71674 AN XY: 74156

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.977

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.971

Alfa AF: 0.986 Hom.: 3815

Bravo AF: 0.965

Asia WGS AF: 0.906 AC: 3152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2973647; hg19: chr5-44390026;