rs10488779

Variant names:

• chr11-80106067-A-G
• rs10488779

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 0.297 in 152,128 control chromosomes in the GnomAD database, including 7,357 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 0.30 (7357 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.297 AC: 45197 AN: 152010 Hom.: 7352 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.297 AC: 45233 AN: 152128 Hom.: 7357 Cov.: 33 AF XY: 0.294 AC XY: 21875 AN XY: 74364

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.281

Alfa AF: 0.244 Hom.: 3752

Bravo AF: 0.300

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488779; hg19: chr11-79817111;