rs2383143

Positions:

• chr9-20649541-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 0.114 in 152,190 control chromosomes in the GnomAD database, including 1,419 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 0.11 (1419 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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: 0.114 AC: 17359 AN: 152072 Hom.: 1415 Cov.: 33

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.114 AC: 17377 AN: 152190 Hom.: 1419 Cov.: 33 AF XY: 0.119 AC XY: 8876 AN XY: 74422

Gnomad4 AFR AF: 0.0267

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.151

Alfa AF: 0.114 Hom.: 137

Bravo AF: 0.117

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2383143; hg19: chr9-20649540; COSMIC: COSV60341272;