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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.333 AC: 13795 AN: 41414

American (AMR) AF: 0.200 AC: 3061 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1783 AN: 5170

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4818

European-Finnish (FIN) AF: 0.158 AC: 1673 AN: 10568

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14239 AN: 67962

Other (OTH) AF: 0.248 AC: 522 AN: 2104

Alfa AF: 0.218 Hom.: 6197

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10816772; hg19: chr9-111885869;