rs1559473

Variant names:

• chr2-222016799-T-G
• rs1559473

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 0.247 in 152,144 control chromosomes in the GnomAD database, including 4,816 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 0.25 (4816 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.247 AC: 37534 AN: 152026 Hom.: 4817 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.247 AC: 37545 AN: 152144 Hom.: 4816 Cov.: 33 AF XY: 0.247 AC XY: 18380 AN XY: 74378

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.254

Alfa AF: 0.264 Hom.: 8810

Bravo AF: 0.236

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1559473; hg19: chr2-222881518;