rs932206

Variant names:

• chr2-136067702-C-T
• rs932206

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 0.35 in 152,084 control chromosomes in the GnomAD database, including 13,205 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 0.35 (13205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.350 AC: 53187 AN: 151966 Hom.: 13206 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.350 AC: 53180 AN: 152084 Hom.: 13205 Cov.: 32 AF XY: 0.337 AC XY: 25069 AN XY: 74342

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.00250

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.269

Alfa AF: 0.455 Hom.: 8073

Bravo AF: 0.321

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.74
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: rs932206; hg19: chr2-136825272;