rs9927309

Variant names:

• chr16-75212521-C-T
• rs9927309

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 0.205 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.369 AC: 15262 AN: 41394

American (AMR) AF: 0.159 AC: 2434 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1052 AN: 5176

South Asian (SAS) AF: 0.166 AC: 799 AN: 4818

European-Finnish (FIN) AF: 0.156 AC: 1649 AN: 10570

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8788 AN: 67994

Other (OTH) AF: 0.207 AC: 436 AN: 2106

Alfa AF: 0.167 Hom.: 5112

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9927309; hg19: chr16-75246419;