rs10488780

Variant names:

• chr11-80101308-C-A
• rs10488780

Your query was ambiguous. Multiple possible variants found:

• chr11-80101308-C-A
• chr11-80101308-C-G
• chr11-80101308-C-T

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 0.227 in 152,030 control chromosomes in the GnomAD database, including 4,115 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 0.23 (4115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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: 0.227 AC: 34437 AN: 151912 Hom.: 4115 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.227 AC: 34447 AN: 152030 Hom.: 4115 Cov.: 32 AF XY: 0.225 AC XY: 16740 AN XY: 74334

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.206

Alfa AF: 0.210 Hom.: 6970

Bravo AF: 0.223

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488780; hg19: chr11-79812352;