chr4-187156658-G-A

Variant names:

• chr4-187156658-G-A
• rs882227

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 0.119 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.117 AC: 4873 AN: 41528

American (AMR) AF: 0.155 AC: 2374 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 470 AN: 3466

East Asian (EAS) AF: 0.0741 AC: 384 AN: 5180

South Asian (SAS) AF: 0.121 AC: 582 AN: 4824

European-Finnish (FIN) AF: 0.172 AC: 1818 AN: 10570

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7355 AN: 68010

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.111 Hom.: 1603

Bravo AF: 0.115

Asia WGS AF: 0.0860 AC: 297 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.18
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs882227; hg19: chr4-188077812;