rs11817364

Variant names:

• chr10-90738269-G-A
• rs11817364

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 0.235 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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

African (AFR) AF: 0.332 AC: 13744 AN: 41378

American (AMR) AF: 0.229 AC: 3498 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3462

East Asian (EAS) AF: 0.167 AC: 860 AN: 5156

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4820

European-Finnish (FIN) AF: 0.174 AC: 1834 AN: 10560

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13469 AN: 67928

Other (OTH) AF: 0.231 AC: 488 AN: 2116

Alfa AF: 0.212 Hom.: 1390

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11817364; hg19: chr10-92498026;