chr3-55455770-G-A

Variant names:

• chr3-55455770-G-A
• rs1499890

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.330 AC: 13694 AN: 41482

American (AMR) AF: 0.565 AC: 8642 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1520 AN: 3468

East Asian (EAS) AF: 0.604 AC: 3119 AN: 5168

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4818

European-Finnish (FIN) AF: 0.390 AC: 4116 AN: 10560

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30828 AN: 67978

Other (OTH) AF: 0.455 AC: 960 AN: 2110

Alfa AF: 0.428 Hom.: 7593

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1499890; hg19: chr3-55489798;