rs7382258

Variant names:

• chr6-31377244-G-A
• rs7382258
• ENST00000755446.1:n.327-4736G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755446.1(ENSG00000298426):​n.327-4736G>A variant causes a intron 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: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 9 publications found

Genes affected

ENSG00000298426 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000298426	ENST00000755446.1	n.327-4736G>A		intron_variant	Intron 1 of 1
ENSG00000298474	ENST00000755731.1	n.303+995C>T		intron_variant	Intron 1 of 1
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

African (AFR) AF: 0.492 AC: 20428 AN: 41482

American (AMR) AF: 0.478 AC: 7319 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3468

East Asian (EAS) AF: 0.572 AC: 2954 AN: 5164

South Asian (SAS) AF: 0.530 AC: 2555 AN: 4822

European-Finnish (FIN) AF: 0.498 AC: 5261 AN: 10564

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41536 AN: 67946

Other (OTH) AF: 0.568 AC: 1198 AN: 2110

Alfa AF: 0.584 Hom.: 19476

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7382258; hg19: chr6-31345021;