rs2168784

Variant names:

• chr3-164872151-C-T
• rs2168784

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 0.232 in 152,044 control chromosomes in the GnomAD database, including 7,407 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 0.23 (7407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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 (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.232 AC: 35191 AN: 151926 Hom.: 7384 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0909

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.232 AC: 35251 AN: 152044 Hom.: 7407 Cov.: 32 AF XY: 0.224 AC XY: 16617 AN XY: 74322

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0909

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.182

Alfa AF: 0.176 Hom.: 605

Bravo AF: 0.252

Asia WGS AF: 0.127 AC: 440 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2168784; hg19: chr3-164589939;