9-122362748-C-T

Variant names:

• chr9-122362748-C-T
• rs883484

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 0.203 in 151,758 control chromosomes in the GnomAD database, including 3,438 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 0.20 (3438 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.203 AC: 30823 AN: 151640 Hom.: 3440 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.203 AC: 30821 AN: 151758 Hom.: 3438 Cov.: 31 AF XY: 0.207 AC XY: 15321 AN XY: 74084

African (AFR) AF: 0.135 AC: 5601 AN: 41408

American (AMR) AF: 0.276 AC: 4196 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 844 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2222 AN: 5132

South Asian (SAS) AF: 0.233 AC: 1116 AN: 4796

European-Finnish (FIN) AF: 0.206 AC: 2164 AN: 10506

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13893 AN: 67924

Other (OTH) AF: 0.208 AC: 438 AN: 2106

Alfa AF: 0.205 Hom.: 1808

Bravo AF: 0.206

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs883484; hg19: chr9-125125027;