rs1889024

Variant names:

• chr17-27733220-A-G
• rs1889024

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 0.559 in 152,042 control chromosomes in the GnomAD database, including 25,202 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 0.56 (25202 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.558 AC: 84849 AN: 151924 Hom.: 25162 Cov.: 33

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.559 AC: 84933 AN: 152042 Hom.: 25202 Cov.: 33 AF XY: 0.558 AC XY: 41470 AN XY: 74336

African (AFR) AF: 0.769 AC: 31903 AN: 41494

American (AMR) AF: 0.571 AC: 8723 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3468

East Asian (EAS) AF: 0.495 AC: 2561 AN: 5176

South Asian (SAS) AF: 0.519 AC: 2501 AN: 4822

European-Finnish (FIN) AF: 0.458 AC: 4847 AN: 10578

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30836 AN: 67930

Other (OTH) AF: 0.553 AC: 1166 AN: 2108

Alfa AF: 0.506 Hom.: 2565

Bravo AF: 0.576

Asia WGS AF: 0.494 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1889024; hg19: chr17-26060246;