rs2883272

Variant names:

• chr1-17446663-G-A
• rs2883272

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 0.199 in 152,208 control chromosomes in the GnomAD database, including 3,176 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 0.20 (3176 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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: 0.199 AC: 30340 AN: 152090 Hom.: 3182 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.199 AC: 30343 AN: 152208 Hom.: 3176 Cov.: 33 AF XY: 0.194 AC XY: 14417 AN XY: 74406

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.233

Alfa AF: 0.229 Hom.: 4285

Bravo AF: 0.207

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2883272; hg19: chr1-17773159;