rs11200572

Variant names:

• chr10-122352022-T-C
• rs11200572

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 0.122 in 152,238 control chromosomes in the GnomAD database, including 1,462 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 0.12 (1462 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18565 AN: 152120 Hom.: 1457 Cov.: 33

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.122 AC: 18579 AN: 152238 Hom.: 1462 Cov.: 33 AF XY: 0.127 AC XY: 9435 AN XY: 74438

African (AFR) AF: 0.0334 AC: 1388 AN: 41578

American (AMR) AF: 0.160 AC: 2442 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 425 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1563 AN: 5168

South Asian (SAS) AF: 0.236 AC: 1138 AN: 4816

European-Finnish (FIN) AF: 0.163 AC: 1730 AN: 10596

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9341 AN: 68008

Other (OTH) AF: 0.118 AC: 248 AN: 2108

Alfa AF: 0.136 Hom.: 595

Bravo AF: 0.119

Asia WGS AF: 0.247 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.050
DANN	Benign	0.55
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11200572; hg19: chr10-124111537;