rs660675

Variant names:

• chr9-21358891-C-A
• rs660675

Your query was ambiguous. Multiple possible variants found:

• chr9-21358891-C-A
• chr9-21358891-C-G
• chr9-21358891-C-T

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 0.165 in 152,102 control chromosomes in the GnomAD database, including 2,141 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 0.16 (2141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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: 0.165 AC: 25039 AN: 151984 Hom.: 2141 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.165 AC: 25050 AN: 152102 Hom.: 2141 Cov.: 32 AF XY: 0.165 AC XY: 12261 AN XY: 74354

African (AFR) AF: 0.158 AC: 6577 AN: 41504

American (AMR) AF: 0.180 AC: 2747 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1520 AN: 5150

South Asian (SAS) AF: 0.0915 AC: 442 AN: 4830

European-Finnish (FIN) AF: 0.176 AC: 1865 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10704 AN: 67982

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.102 Hom.: 180

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.31
DANN	Benign	0.36
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs660675; hg19: chr9-21358890;