rs16824684

Positions:

• chr3-155196301-T-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 0.231 in 152,098 control chromosomes in the GnomAD database, including 4,320 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 (4320 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 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: 0.231 AC: 35136 AN: 151980 Hom.: 4316 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.231 AC: 35164 AN: 152098 Hom.: 4320 Cov.: 33 AF XY: 0.231 AC XY: 17175 AN XY: 74360

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.224

Alfa AF: 0.214 Hom.: 1682

Bravo AF: 0.227

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16824684; hg19: chr3-154914090;