rs7382258

Variant names:

• chr6-31377244-G-A
• rs7382258
• ENST00000449999.1:n.-175G>A

Variant summary

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

The ENST00000449999.1(FGFR3P1):​n.-175G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,064 control chromosomes in the GnomAD database, including 23,228 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 0.55 (23228 hom., cov: 31)
• Consequence: FGFR3P1 ENST00000449999.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFR3P1	ENST00000449999.1	n.-175G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83329 AN: 151946 Hom.: 23218 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.548 AC: 83376 AN: 152064 Hom.: 23228 Cov.: 31 AF XY: 0.542 AC XY: 40304 AN XY: 74342

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.568

Alfa AF: 0.584 Hom.: 14447

Bravo AF: 0.545

Asia WGS AF: 0.472 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7382258; hg19: chr6-31345021;