rs10816772

Variant names:

• chr9-109123589-T-C
• rs10816772

Your query was ambiguous. Multiple possible variants found:

• chr9-109123589-T-C
• chr9-109123589-T-G

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 0.246 in 152,000 control chromosomes in the GnomAD database, including 5,003 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 0.25 (5003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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: 0.246 AC: 37319 AN: 151882 Hom.: 4987 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.246 AC: 37376 AN: 152000 Hom.: 5003 Cov.: 32 AF XY: 0.244 AC XY: 18156 AN XY: 74300

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.248

Alfa AF: 0.215 Hom.: 4726

Bravo AF: 0.252

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10816772; hg19: chr9-111885869;