9-86904118-C-T

Variant names:

• chr9-86904118-C-T
• rs10512177

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 0.22 in 152,182 control chromosomes in the GnomAD database, including 3,992 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 0.22 (3992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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: 0.220 AC: 33508 AN: 152064 Hom.: 3991 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0562

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.220 AC: 33516 AN: 152182 Hom.: 3992 Cov.: 32 AF XY: 0.220 AC XY: 16355 AN XY: 74400

African (AFR) AF: 0.147 AC: 6090 AN: 41518

American (AMR) AF: 0.224 AC: 3433 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3466

East Asian (EAS) AF: 0.0564 AC: 292 AN: 5180

South Asian (SAS) AF: 0.245 AC: 1181 AN: 4822

European-Finnish (FIN) AF: 0.262 AC: 2779 AN: 10590

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18053 AN: 67994

Other (OTH) AF: 0.238 AC: 503 AN: 2112

Alfa AF: 0.246 Hom.: 6925

Bravo AF: 0.210

Asia WGS AF: 0.122 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.19
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10512177; hg19: chr9-89519033;