rs11200580

chr10-122361826-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;