rs11200580

Variant names:

• chr10-122361826-A-G
• rs11200580

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 0.255 in 151,950 control chromosomes in the GnomAD database, including 5,776 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 0.26 (5776 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 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: 0.255 AC: 38731 AN: 151832 Hom.: 5762 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.255 AC: 38754 AN: 151950 Hom.: 5776 Cov.: 31 AF XY: 0.263 AC XY: 19531 AN XY: 74234

Gnomad4 AFR AF: 0.0999

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.258

Alfa AF: 0.290 Hom.: 2115

Bravo AF: 0.245

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11200580; hg19: chr10-124121342;