rs2973649

Variant names:

• chr5-44391059-T-G
• rs2973649
• ENST00000502457.1:n.182+2146T>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.182+2146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,100 control chromosomes in the GnomAD database, including 44,028 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 0.76 (44028 hom., cov: 33)
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF10-AS1	NR_108034.1	n.182+2146T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF10-AS1	ENST00000502457.1	n.182+2146T>G		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115370 AN: 151982 Hom.: 44007 Cov.: 33

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.759 AC: 115430 AN: 152100 Hom.: 44028 Cov.: 33 AF XY: 0.760 AC XY: 56500 AN XY: 74348

African (AFR) AF: 0.719 AC: 29812 AN: 41476

American (AMR) AF: 0.678 AC: 10370 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2795 AN: 3472

East Asian (EAS) AF: 0.709 AC: 3663 AN: 5166

South Asian (SAS) AF: 0.775 AC: 3737 AN: 4820

European-Finnish (FIN) AF: 0.769 AC: 8134 AN: 10580

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54362 AN: 67982

Other (OTH) AF: 0.769 AC: 1626 AN: 2114

Alfa AF: 0.785 Hom.: 22707

Bravo AF: 0.749

Asia WGS AF: 0.647 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
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: rs2973649; hg19: chr5-44391161;