rs882227

Positions:

• chr4-187156658-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;