3-184655299-C-T

Variant names:

• chr3-184655299-C-T
• rs3890724

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 0.0606 in 152,146 control chromosomes in the GnomAD database, including 855 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 0.061 (855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.0604 AC: 9182 AN: 152028 Hom.: 850 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.00663

Gnomad FIN AF: 0.000566

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00525

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0606 AC: 9218 AN: 152146 Hom.: 855 Cov.: 32 AF XY: 0.0580 AC XY: 4314 AN XY: 74400

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0230

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.00560

Gnomad4 SAS AF: 0.00643

Gnomad4 FIN AF: 0.000566

Gnomad4 NFE AF: 0.00525

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.00323 Hom.: 4

Bravo AF: 0.0692

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3890724; hg19: chr3-184373087;