rs2507984

Positions:

• chr6-31377819-G-A

Variant summary

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

The ENST00000449999.1(FGFR3P1):​n.401G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 157,518 control chromosomes in the GnomAD database, including 5,023 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 0.23 (4980 hom., cov: 32)
  • Exomes 𝑓: 0.12 (43 hom.)
• Consequence: FGFR3P1 ENST00000449999.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

Genes affected

FGFR3P1 (HGNC:21664): (fibroblast growth factor receptor 3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFR3P1	ENST00000449999.1	n.401G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35096 AN: 151972 Hom.: 4979 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.119 AC: 648 AN: 5428 Hom.: 43 Cov.: 0 AF XY: 0.123 AC XY: 329 AN XY: 2684

Gnomad4 AFR exome AF: 0.0417

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.104

Gnomad4 FIN exome AF: 0.113

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.231 AC: 35113 AN: 152090 Hom.: 4980 Cov.: 32 AF XY: 0.223 AC XY: 16616 AN XY: 74348

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.190

Alfa AF: 0.280 Hom.: 3212

Bravo AF: 0.213

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	13
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2507984; hg19: chr6-31345596;