rs2383183

chr9-21187701-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 0.099 in 1,089,644 control chromosomes in the GnomAD database, including 5,658 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 0.080 (657 hom., cov: 32)
  • Exomes 𝑓: 0.10 (5001 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 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: 0.0798 AC: 12151 AN: 152190 Hom.: 656 Cov.: 32

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0823

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0790

GnomAD4 exome AF: 0.102 AC: 95678 AN: 937336 Hom.: 5001 Cov.: 13 AF XY: 0.101 AC XY: 46510 AN XY: 459970

Gnomad4 AFR exome AF: 0.0147

Gnomad4 AMR exome AF: 0.0714

Gnomad4 ASJ exome AF: 0.0976

Gnomad4 EAS exome AF: 0.165

Gnomad4 SAS exome AF: 0.0541

Gnomad4 FIN exome AF: 0.106

Gnomad4 NFE exome AF: 0.106

Gnomad4 OTH exome AF: 0.0946

GnomAD4 genome AF: 0.0798 AC: 12159 AN: 152308 Hom.: 657 Cov.: 32 AF XY: 0.0803 AC XY: 5978 AN XY: 74460

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0515

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0911 Hom.: 144

Bravo AF: 0.0739

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.57
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2383183; hg19: chr9-21187700; COSMIC: COSV70179660;