rs16832011

Positions:

• chr2-135787729-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 0.0489 in 156,138 control chromosomes in the GnomAD database, including 346 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 0.050 (345 hom., cov: 32)
  • Exomes 𝑓: 0.013 (1 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135787729A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0498 AC: 7580 AN: 152118 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.0591

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0407

GnomAD4 exome AF: 0.0131 AC: 51 AN: 3902 Hom.: 1 AF XY: 0.0141 AC XY: 29 AN XY: 2064

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0167

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0500

Gnomad4 SAS exome AF: 0.00995

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0114

Gnomad4 OTH exome AF: 0.00725

GnomAD4 genome AF: 0.0498 AC: 7587 AN: 152236 Hom.: 345 Cov.: 32 AF XY: 0.0485 AC XY: 3612 AN XY: 74452

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.0592

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0224

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0286 Hom.: 182

Bravo AF: 0.0538

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16832011; hg19: chr2-136545299;