rs2383145

Variant names:

• chr9-20649912-A-C
• rs2383145

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 0.116 in 152,202 control chromosomes in the GnomAD database, including 1,446 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 0.12 (1446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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: 0.116 AC: 17615 AN: 152084 Hom.: 1442 Cov.: 32

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.116 AC: 17632 AN: 152202 Hom.: 1446 Cov.: 32 AF XY: 0.121 AC XY: 8980 AN XY: 74396

Gnomad4 AFR AF: 0.0272

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.154

Alfa AF: 0.124 Hom.: 498

Bravo AF: 0.119

Asia WGS AF: 0.196 AC: 680 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2383145; hg19: chr9-20649911; COSMIC: COSV60341290;