rs11573959

chr8-118922023-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.163 in 152,008 control chromosomes in the GnomAD database, including 2,099 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 (2099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24779 AN: 151890 Hom.: 2095 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.163 AC: 24803 AN: 152008 Hom.: 2099 Cov.: 31 AF XY: 0.161 AC XY: 11929 AN XY: 74310

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.194

Alfa AF: 0.158 Hom.: 227

Bravo AF: 0.167

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.86
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11573959; hg19: chr8-119934262; COSMIC: COSV52074833;