rs9960523

Variant names:

• chr18-9456984-C-T
• rs9960523

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 0.314 in 151,996 control chromosomes in the GnomAD database, including 7,708 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 0.31 (7708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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: 0.314 AC: 47693 AN: 151878 Hom.: 7697 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.314 AC: 47747 AN: 151996 Hom.: 7708 Cov.: 32 AF XY: 0.315 AC XY: 23414 AN XY: 74280

African (AFR) AF: 0.296 AC: 12247 AN: 41434

American (AMR) AF: 0.256 AC: 3915 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3470

East Asian (EAS) AF: 0.143 AC: 737 AN: 5170

South Asian (SAS) AF: 0.278 AC: 1340 AN: 4814

European-Finnish (FIN) AF: 0.449 AC: 4732 AN: 10548

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23008 AN: 67964

Other (OTH) AF: 0.300 AC: 632 AN: 2110

Alfa AF: 0.319 Hom.: 11892

Bravo AF: 0.297

Asia WGS AF: 0.200 AC: 698 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	0.32
DANN	Benign	0.47
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs9960523; hg19: chr18-9456982;