chr8-118922023-C-T

Variant names:

• chr8-118922023-C-T
• rs11573959

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 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

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;