rs11817364

Variant names:

• chr10-90738269-G-A
• rs11817364

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 0.235 in 151,882 control chromosomes in the GnomAD database, including 4,522 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 0.24 (4522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.235 AC: 35705 AN: 151764 Hom.: 4515 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.235 AC: 35742 AN: 151882 Hom.: 4522 Cov.: 32 AF XY: 0.234 AC XY: 17383 AN XY: 74226

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.231

Alfa AF: 0.209 Hom.: 1096

Bravo AF: 0.242

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.36
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11817364; hg19: chr10-92498026;