rs2320289

Positions:

• chr4-18160481-A-C
• chr4-18160481-A-G

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 0.211 in 152,126 control chromosomes in the GnomAD database, including 3,629 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 0.21 (3629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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: 0.211 AC: 32044 AN: 152008 Hom.: 3611 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.211 AC: 32081 AN: 152126 Hom.: 3629 Cov.: 33 AF XY: 0.214 AC XY: 15935 AN XY: 74376

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.229

Alfa AF: 0.193 Hom.: 2902

Bravo AF: 0.222

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	2.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2320289; hg19: chr4-18162104;