rs882227

Variant names:

• chr4-187156658-G-A
• rs882227

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 0.119 in 152,182 control chromosomes in the GnomAD database, including 1,151 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 0.12 (1151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 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: 0.119 AC: 18147 AN: 152064 Hom.: 1148 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0745

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.119 AC: 18161 AN: 152182 Hom.: 1151 Cov.: 33 AF XY: 0.123 AC XY: 9143 AN XY: 74398

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0741

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.102

Alfa AF: 0.110 Hom.: 1252

Bravo AF: 0.115

Asia WGS AF: 0.0860 AC: 297 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs882227; hg19: chr4-188077812;