rs11206237

chr1-53890688-C-A

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 0.159 in 452,482 control chromosomes in the GnomAD database, including 6,483 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 0.13 (1471 hom., cov: 32)
  • Exomes 𝑓: 0.17 (5012 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 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: 0.131 AC: 19947 AN: 152058 Hom.: 1472 Cov.: 32

Gnomad AFR AF: 0.0668

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.146

GnomAD4 exome AF: 0.174 AC: 52192 AN: 300306 Hom.: 5012 AF XY: 0.179 AC XY: 30521 AN XY: 170718

Gnomad4 AFR exome AF: 0.0671

Gnomad4 AMR exome AF: 0.222

Gnomad4 ASJ exome AF: 0.183

Gnomad4 EAS exome AF: 0.172

Gnomad4 SAS exome AF: 0.238

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.157

GnomAD4 genome AF: 0.131 AC: 19930 AN: 152176 Hom.: 1471 Cov.: 32 AF XY: 0.132 AC XY: 9813 AN XY: 74412

Gnomad4 AFR AF: 0.0666

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.144

Alfa AF: 0.141 Hom.: 269

Bravo AF: 0.132

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.7
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11206237; hg19: chr1-54356361; COSMIC: COSV50779094;