dbSNP rs2507984: FGFR3P1:n.401G>A (chr6-31377819-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.221

Publications

14 publications found

Variant links:

Genes affected

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

FGFR3P1 links:

ENSG00000298426 (HGNC:):

ENSG00000298426 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000449999.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449999.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
FGFR3P1	ENST00000449999.1	TSL:6	n.401G>A	non_coding_transcript_exon	Exon 1 of 1
ENSG00000298426	ENST00000755446.1		n.327-4161G>A	intron	N/A
ENSG00000298474	ENST00000755731.1		n.303+420C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

35096

AN:

151972

Hom.:

4979

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.123

AC XY:

329

AN XY:

2684

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0417

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.104

AC:

AN:

624

European-Finnish (FIN)

AF:

0.113

AC:

476

AN:

4196

Middle Eastern (MID)

AF:

0.0556

AC:

AN:

162

European-Non Finnish (NFE)

AF:

0.256

AC:

AN:

340

Other (OTH)

AF:

0.113

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.395

Heterozygous variant carriers

110

138

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.231

AC:

35113

AN:

152090

Hom.:

4980

Cov.:

AF XY:

0.223

AC XY:

16616

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.104

AC:

4308

AN:

41516

American (AMR)

AF:

0.141

AC:

2164

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

439

AN:

3470

East Asian (EAS)

AF:

0.220

AC:

1135

AN:

5164

South Asian (SAS)

AF:

0.140

AC:

673

AN:

4816

European-Finnish (FIN)

AF:

0.287

AC:

3031

AN:

10570

Middle Eastern (MID)

AF:

0.182

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.332

AC:

22585

AN:

67934

Other (OTH)

AF:

0.190

AC:

403

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1307

2614

3921

5228

6535

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

372

744

1116

1488

1860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.293

Hom.:

17171

Bravo

AF:

0.213

Asia WGS

AF:

0.169

AC:

587

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

(source)

DANN

Benign

0.61

PhyloP100

0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over