rs1499890

Positions:

• chr3-55455770-G-A
• chr3-55455770-G-C

Variant summary

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

The variant allele was found at a frequency of 0.431 in 152,078 control chromosomes in the GnomAD database, including 14,664 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 0.43 (14664 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65477 AN: 151960 Hom.: 14658 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.431 AC: 65495 AN: 152078 Hom.: 14664 Cov.: 33 AF XY: 0.431 AC XY: 32046 AN XY: 74320

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.455

Alfa AF: 0.424 Hom.: 6679

Bravo AF: 0.442

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1499890; hg19: chr3-55489798;