rs9927309

Variant names:

• chr16-75212521-C-T
• rs9927309

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 0.205 in 152,004 control chromosomes in the GnomAD database, including 4,005 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 0.21 (4005 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.205 AC: 31110 AN: 151888 Hom.: 3982 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.205 AC: 31166 AN: 152004 Hom.: 4005 Cov.: 31 AF XY: 0.204 AC XY: 15151 AN XY: 74288

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.207

Alfa AF: 0.148 Hom.: 2514

Bravo AF: 0.213

Asia WGS AF: 0.205 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
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: rs9927309; hg19: chr16-75246419;