rs11573959

Variant names:

• chr8-118922023-C-T
• rs11573959

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 0.163 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.162 AC: 6732 AN: 41450

American (AMR) AF: 0.162 AC: 2474 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3470

East Asian (EAS) AF: 0.138 AC: 716 AN: 5172

South Asian (SAS) AF: 0.184 AC: 884 AN: 4808

European-Finnish (FIN) AF: 0.123 AC: 1297 AN: 10564

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11411 AN: 67962

Other (OTH) AF: 0.194 AC: 406 AN: 2098

Alfa AF: 0.158 Hom.: 239

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

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