rs1203833

chr16-168533-T-C

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 0.206 in 152,092 control chromosomes in the GnomAD database, including 3,360 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 (3359 hom., cov: 32)
  • Exomes 𝑓: 0.24 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31293 AN: 151870 Hom.: 3357 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.240 AC: 24 AN: 100 Hom.: 1 AF XY: 0.250 AC XY: 18 AN XY: 72

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.237

GnomAD4 genome AF: 0.206 AC: 31318 AN: 151992 Hom.: 3359 Cov.: 32 AF XY: 0.205 AC XY: 15245 AN XY: 74312

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.209

Alfa AF: 0.204 Hom.: 490

Bravo AF: 0.213

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.27
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1203833; hg19: chr16-218532; COSMIC: COSV52406424;