9-20649912-A-C

Position:

• chr9-20649912-A-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 0.116 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;