chr9-21174644-C-T

Variant names:

• chr9-21174644-C-T
• rs7852323

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 0.209 in 152,120 control chromosomes in the GnomAD database, including 3,676 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 0.21 (3676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• 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 = 0.404 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: 0.209 AC: 31706 AN: 152002 Hom.: 3669 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.209 AC: 31758 AN: 152120 Hom.: 3676 Cov.: 32 AF XY: 0.210 AC XY: 15604 AN XY: 74358

African (AFR) AF: 0.248 AC: 10297 AN: 41478

American (AMR) AF: 0.250 AC: 3820 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2162 AN: 5168

South Asian (SAS) AF: 0.112 AC: 541 AN: 4830

European-Finnish (FIN) AF: 0.198 AC: 2091 AN: 10578

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11565 AN: 67990

Other (OTH) AF: 0.207 AC: 437 AN: 2112

Alfa AF: 0.200 Hom.: 526

Bravo AF: 0.217

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs7852323; hg19: chr9-21174643;