rs2883272

Variant names:

• chr1-17446663-G-A
• rs2883272

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 0.199 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.179 AC: 7427 AN: 41526

American (AMR) AF: 0.221 AC: 3375 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.0526 AC: 273 AN: 5186

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4818

European-Finnish (FIN) AF: 0.123 AC: 1307 AN: 10606

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15140 AN: 68004

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.218 Hom.: 13235

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2883272; hg19: chr1-17773159;