rs932206

chr2-136067702-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;