rs11189328

Variant names:

• chr10-97688247-C-T
• rs11189328

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 0.195 in 151,980 control chromosomes in the GnomAD database, including 2,988 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 0.19 (2988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29524 AN: 151862 Hom.: 2982 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.195 AC: 29561 AN: 151980 Hom.: 2988 Cov.: 32 AF XY: 0.192 AC XY: 14300 AN XY: 74312

African (AFR) AF: 0.193 AC: 8007 AN: 41438

American (AMR) AF: 0.190 AC: 2904 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1060 AN: 5170

South Asian (SAS) AF: 0.290 AC: 1398 AN: 4814

European-Finnish (FIN) AF: 0.110 AC: 1167 AN: 10574

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

European-Non Finnish (NFE) AF: 0.199 AC: 13551 AN: 67940

Other (OTH) AF: 0.204 AC: 428 AN: 2100

Alfa AF: 0.201 Hom.: 12391

Bravo AF: 0.199

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs11189328; hg19: chr10-99448004;