rs13084057

Positions:

• chr3-46143233-C-G
• chr3-46143233-C-T

Variant summary

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

The ENST00000451650.1(FLT1P1):​n.445G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.114 in 789,390 control chromosomes in the GnomAD database, including 6,931 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 0.097 (831 hom., cov: 32)
  • Exomes 𝑓: 0.12 (6100 hom.)
• Consequence: FLT1P1 ENST00000451650.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.13

Genes affected

FLT1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLT1P1		n.46143233C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT1P1	ENST00000451650.1	n.445G>C		non_coding_transcript_exon_variant	1/1	6
CCR3	ENST00000684109.1	n.691+11653C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14750 AN: 152150 Hom.: 829 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.0855

GnomAD4 exome AF: 0.118 AC: 74983 AN: 637122 Hom.: 6100 Cov.: 6 AF XY: 0.127 AC XY: 43844 AN XY: 346038

Gnomad4 AFR exome AF: 0.111

Gnomad4 AMR exome AF: 0.0556

Gnomad4 ASJ exome AF: 0.113

Gnomad4 EAS exome AF: 0.0477

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.154

Gnomad4 NFE exome AF: 0.0964

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.0969 AC: 14762 AN: 152268 Hom.: 831 Cov.: 32 AF XY: 0.104 AC XY: 7715 AN XY: 74456

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0627

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0447

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.0851

Alfa AF: 0.0437 Hom.: 36

Bravo AF: 0.0860

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	10
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13084057; hg19: chr3-46184725;