rs2383145

Variant names:

• chr9-20649912-A-C
• rs2383145

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0272 AC: 1130 AN: 41566

American (AMR) AF: 0.215 AC: 3288 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1338 AN: 5170

South Asian (SAS) AF: 0.142 AC: 687 AN: 4824

European-Finnish (FIN) AF: 0.163 AC: 1724 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8456 AN: 68006

Other (OTH) AF: 0.154 AC: 326 AN: 2114

Alfa AF: 0.122 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
PhyloP100		-1.2

Splicing

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

Other links and lift over

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