9-21229185-C-T

Variant names:

• chr9-21229185-C-T
• rs10964920

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 0.237 in 151,986 control chromosomes in the GnomAD database, including 4,970 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 0.24 (4970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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: 0.237 AC: 36054 AN: 151868 Hom.: 4964 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.237 AC: 36090 AN: 151986 Hom.: 4970 Cov.: 32 AF XY: 0.239 AC XY: 17745 AN XY: 74296

African (AFR) AF: 0.324 AC: 13446 AN: 41454

American (AMR) AF: 0.274 AC: 4191 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2680 AN: 5168

South Asian (SAS) AF: 0.186 AC: 895 AN: 4824

European-Finnish (FIN) AF: 0.193 AC: 2041 AN: 10560

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11489 AN: 67922

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.107 Hom.: 177

Bravo AF: 0.249

Asia WGS AF: 0.327 AC: 1135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.45
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs10964920; hg19: chr9-21229184;